| Journal/Book Conference Report Abstract/Poster |
@article { Balin25-TMLR,
arxiv = { 2310.12403 },
note = { Also available as a Tech Rep on {ArXiv}. },
journal = { Transactions on Machine Learning Research (TMLR) },
url = { https://openreview.net/pdf?id=f6yMdmrD2g },
month = { Jan },
year = { 2025 },
title = { Cooperative Minibatching in Graph Neural Networks },
author = { Muhammed Fatih Bal{\i}n and Dominique LaSalle and \"Umit V. \c{C}ataly\"{u}rek },
}
@inproceedings { SANCAK25-AAAI,
note = { To appear. Also available as a Tech Rep on {ArXiv}. },
year = { 2025 },
booktitle = { Proceedings of the AAAI Conference on Artificial Intelligence },
author = { Kaan Sancak and Zhigang Hua and Jin Fang and Yan Xie and Andrey Malevich and Bo Long and Muhammed Fatih Bal{\i}n and \"Umit V. \c{C}ataly\"{u}rek },
title = { A Scalable and Effective Alternative to Graph Transformers },
}
@techreport { SANCAK25-ARXIV-GECO,
arxiv = { 2406.12059 },
number = { arXiv:2406.12059 },
month = { June },
institution = { ArXiv },
url = { https://arxiv.org/abs/2406.12059 },
year = { 2024 },
booktitle = { Proceedings of the AAAI Conference on Artificial Intelligence },
author = { Kaan Sancak and Zhigang Hua and Jin Fang and Yan Xie and Andrey Malevich and Bo Long and Muhammed Fatih Bal{\i}n and \"Umit V. \c{C}ataly\"{u}rek },
title = { A Scalable and Effective Alternative to Graph Transformers },
}
@inproceedings { SANCAK24-LoG,
url = { https://openreview.net/forum?id=0664MgKEVz },
year = { 2024 },
booktitle = { The Third Learning on Graphs Conference },
author = { Kaan Sancak and Muhammed Fatih Bal{\i}n and \"Umit V. \c{C}ataly\"{u}rek },
title = { Do We Really Need Complicated Graph Learning Models? -- A Simple but Effective Baseline },
}
@techreport { Balin23-ARXIV-SGORP,
arxiv = { 2310.02470 },
number = { arXiv:2310.02470 },
month = { October },
year = { 2023 },
institution = { ArXiv },
url = { https://arxiv.org/abs/2310.02470 },
author = { Muhammed Fatih Bal{\i}n and Xiaojing An and Abdurrahman Ya\c{s}ar and \"Umit V. \c{C}ataly\"{u}rek },
title = { SGORP: A Subgradient-based Method for d-Dimensional Rectilinear Partitioning },
}
@techreport { Balin23-ARXIV-COOPERATIVE,
arxiv = { 2310.12403 },
number = { arXiv:2310.12403 },
month = { October },
year = { 2023 },
institution = { ArXiv },
url = { https://arxiv.org/abs/2310.12403 },
author = { Muhammed Fatih Bal{\i}n and Dominique LaSalle and \"Umit V. \c{C}ataly\"{u}rek },
title = { Cooperative Minibatching in Graph Neural Networks },
}
@inproceedings { Balin23-NeurIPS,
arxiv = { 2210.13339 },
note = { Also available as a Tech Rep on {ArXiv}. },
booktitle = { Advances in Neural Information Processing Systems (NeurIPS) },
url = { https://openreview.net/pdf?id=Kd5W4JRsfV },
month = { Dec },
year = { 2023 },
title = { Layer-Neighbor Sampling --- Defusing Neighborhood Explosion in GNNs },
author = { Muhammed Fatih Bal{\i}n and \"Umit V. \c{C}ataly\"{u}rek },
}
@inproceedings { Nisa23-GRAPL,
doi = { 10.1109/IPDPSW59300.2023.00042 },
booktitle = { 2023 IEEE International Parallel and Distributed Processing Symposium Workshops (IPDPSW), Workshop on Graphs, Architectures, Programming, and Learning (GrAPL) },
url = { https://www.amazon.science/publications/optimizing-irregular-dense-operators-of-heterogeneous-gnn-models-on-gpu },
year = { 2023 },
title = { Optimizing irregular dense operators of heterogeneous GNN models on GPU },
author = { Israt Nisa and Minjie Wang and Da Zheng and Qiang Fu and \"Umit V. \c{C}ataly\"{u}rek and George Karypis },
}
@article { Catalyurek22-CSUR,
doi = { 10.1145/3571808 },
url = { https://dl.acm.org/doi/10.1145/3571808 },
number = { 12 },
volume = { 55 },
year = { 2023 },
journal = { ACM Computing Surveys },
title = { More Recent Advances in (Hyper)Graph Partitioning },
author = { \"Umit V. \c{C}ataly\"{u}rek and Karen D. Devine and Marcelo Fonseca Faraj and Lars Gottesb\"{u}ren and Tobias Heuer and Henning Meyerhenke and Peter Sanders and Sebastian Schlag and Christian Schulz and Daniel Seemaier and Dorothea Wagner },
}
@inproceedings { Rabi22-HiPC,
doi = { 10.1109/HiPC56025.2022.00030 },
year = { 2022 },
month = { Dec },
booktitle = { 29th IEEE International Conference on High Performance Computing, Data, \& Analytics (HiPC 2022) },
title = { Portable Sparse Solver Framework for Large Matrices on Heterogeneous Architectures },
author = { Fazlay Rabbi and Christopher S. Daley and {\"U}mit V. \c{C}ataly\"{u}rek and Hasan Metin Aktulga },
}
@article { An22-iScience,
url = { https://www.sciencedirect.com/science/article/pii/S2589004222015450 },
doi = { 10.1016/j.isci.2022.105273 },
issn = { 2589-0042 },
year = { 2022 },
pages = { 105273 },
number = { 11 },
volume = { 25 },
journal = { iScience },
author = { Xiaojing An and Priyanka Ghosh and Patrick Keppler and Sureyya Emre Kurt and Sriram Krishnamoorthy and Ponnuswamy Sadayappan and Aravind Sukumaran Rajam and \"Umit V. \c{C}ataly\"{u}rek and Ananth Kalyanaraman },
title = { BOA: A partitioned view of genome assembly },
}
@techreport { Yasar22-ARXIV,
arxiv = { 2209.04541 },
number = { arXiv:2209.04541 },
month = { September },
year = { 2022 },
institution = { ArXiv },
url = { https://arxiv.org/abs/2209.04541 },
author = { Abdurrahman Ya\c{s}ar and Sivasankaran Rajamanickam and Jonathan W. Berry and {\"U}mit V. \c{C}ataly\"{u}rek },
title = { PGAbB: A Block-Based Graph Processing Framework for Heterogeneous Platforms },
}
@article { Yasar22-JEA,
doi = { 10.1145/3523750 },
volume = { 27 },
month = { Dec },
journal = { Journal of Experimental Algorithmics },
year = { 2022 },
author = { Abdurrahman Ya\c{s}ar and Muhammed Fatih Bal{\i}n and Xiaojing An and Kaan Sancak and {\"U}mit V. \c{C}ataly\"{u}rek },
title = { On Symmetric Rectilinear Matrix Partitioning },
}
@inproceedings { Fang22-Cluster,
doi = { 10.1109/CLUSTER51413.2022.00041 },
note = { Best Paper Award },
optdoi = { },
booktitle = { IEEE International Conference on Cluster Computing },
month = { Sep },
year = { 2022 },
author = { Bo Fang and M. Yusuf \"{O}zkaya and Ang Li and {\"U}mit V. \c{C}ataly\"{u}rek and Sriram Krishnamoorthy },
title = { Efficient Hierarchical State Vector Simulation of Quantum Circuits via Acyclic Graph Partitioning },
}
@inproceedings { Balin22-ICPP,
arxiv = { 2110.08688 },
note = { Also available as a Tech Rep on {ArXiv}. },
doi = { 10.1145/3545008.3545082 },
month = { Aug },
year = { 2022 },
booktitle = { Proc. of 51st Int{\'}l. Conf. on Parallel Processing (ICPP) },
title = { MG-GCN: Scalable Multi-GPU Full Batch GCN Training Framework },
author = { Muhammed Fatih Bal{\i}n and Kaan Sancak and {\"U}mit V. \c{C}ataly\"{u}rek },
}
@techreport { Ozkaya22-ARXIV,
arxiv = { 2207.13638 },
number = { arXiv:2207.13638 },
month = { July },
year = { 2022 },
institution = { ArXiv },
url = { https://arxiv.org/abs/2207.13638 },
doi = { 10.48550/ARXIV.2207.13638 },
author = { M. Yusuf \"{O}zkaya and {\"U}mit V. \c{C}ataly\"{u}rek },
title = { A Simple and Elegant Mathematical Formulation for the Acyclic DAG Partitioning Problem },
}
@inproceedings { Cobb22-PASC,
doi = { 10.1145/3539781.3539798 },
booktitle = { Platform for Advanced Scientific Computing (PASC) },
month = { Jun },
year = { 2022 },
author = { Benjamin Cobb and Hemanth Kolla and Eric Phipps and {\"U}mit V. \c{C}ataly\"{u}rek },
title = { {FIST-HOSVD}: Fused In-place Sequentially Truncated Higher Order Singular Value Decomposition },
}
@inproceedings { Gabert22-GRADES-NDA,
doi = { 10.1145/3534540.3534694 },
booktitle = { Proceedings of the 5th ACM SIGMOD Joint International Workshop on Graph Data Management Experiences \& Systems (GRADES) and Network Data Analytics (NDA) },
month = { Jun },
year = { 2022 },
author = { Kasimir Gabert and Ali P{\i}nar and {\"U}mit V. \c{C}ataly\"{u}rek },
title = { Batch Dynamic Algorithm to Find k-Core Hierarchies },
}
@misc { Priyanka22-RECOMB-SEQ,
url = { https://www.biorxiv.org/content/10.1101/2022.05.22.492973v1 },
note = { non-archival. },
howpublished = { Recomb-Seq 2022-12th RECOMB Satellite Workshop on Massively Parallel Sequencing },
month = { May },
year = { 2022 },
author = { Priyanka Ghosh and Xiaojing An and Patrick Keppler and Sureyya Emre Kurt and {\"U}mit V. \c{C}ataly\"urek and Sriram Krishnamoorthy and P. Sadayappan and Aravind Sukumaran Rajam and Ananth Kalyanaraman },
title = { BOA: A Partitioned View of Genome Assembly },
}
@techreport { Fang22-ARXIV,
url = { https://arxiv.org/abs/2205.06973 },
doi = { 10.48550/ARXIV.2205.06973 },
arxiv = { 2205.06973 },
number = { arXiv:2205.06973 },
month = { May },
year = { 2022 },
institution = { ArXiv },
author = { Bo Fang and M. Yusuf \"{O}zkaya and Ang Li and {\"U}mit V. \c{C}ataly\"{u}rek and Sriram Krishnamoorthy },
title = { Efficient Hierarchical State Vector Simulation of Quantum Circuits via Acyclic Graph Partitioning },
}
@phdthesis { Gabert22-PhD,
year = { 2022 },
title = { Finding Dense Regions of Rapidly Changing Graphs },
month = { May },
institution = { Georgia Institute of Technology, School of Computational Science and Engineering },
author = { Kasimir Gabert },
}
@techreport { Gabert22-ARXIV-CORES,
note = { preprint of Gabert22-GRADES-NDA. },
url = { http://arxiv.org/abs/2203.13095 },
arxiv = { 2203.13095 },
number = { arXiv:2203.13095 },
month = { Mar },
year = { 2022 },
institution = { ArXiv },
author = { Kasimir Gabert and Ali P{\i}nar and {\"U}mit V. \c{C}ataly\"{u}rek },
title = { Batch Dynamic Algorithm to Find k-Cores and Hierarchies },
}
@article { Yasar22-TPDS,
doi = { 10.1109/TPDS.2021.3093240 },
pages = { 444-458 },
number = { 2 },
volume = { 33 },
month = { Feb },
year = { 2022 },
journal = { IEEE Transactions on Parallel and Distributed Systems },
author = { Abdurrahman Ya\c{s}ar and Sivasankaran Rajamanickam and Jonathan W. Berry and {\"U}mit V. \c{C}ataly\"{u}rek },
title = { A Block-Based Triangle Counting Algorithm on Heterogeneous Environments },
}
@phdthesis { Yasar21-PhD,
year = { 2021 },
title = { Towards Performance Portable Graph Algorithms },
month = { Sep },
institution = { Georgia Institute of Technology, School of Computational Science and Engineering },
author = { Abdurrahman Ya\c{s}ar },
}
@inproceedings { An21-HiPC,
doi = { 10.1109/HiPC53243.2021.00034 },
booktitle = { HiPC21: 28th IEEE International Conference on High Performance Computing, Data, \& Analytics },
month = { Dec },
year = { 2021 },
author = { Xiaojing An and {\"U}mit V. \c{C}ataly\"{u}rek },
title = { Column-Segmented Sparse Matrix-Matrix Multiplication },
}
@inproceedings { Gabert21-SC,
doi = { 10.1145/3458817.3480857 },
booktitle = { SC21: International Conference for High Performance Computing, Networking, Storage and Analysis },
month = { Nov },
year = { 2021 },
author = { Kasimir Gabert and Kaan Sancak and M. Yusuf \"{O}zkaya and Ali P{\i}nar and {\"U}mit V. \c{C}ataly\"{u}rek },
title = { {ElGA}: Elastic and Scalable Dynamic Graph Analysis },
}
@inproceedings { Alperen21-ICPP,
doi = { 10.1145/3472456.3472476 },
month = { Aug },
year = { 2021 },
booktitle = { Proc. of 50th Int{\'}l. Conf. on Parallel Processing (ICPP) },
title = { An Evaluation of Task-Parallel Frameworks for Sparse Solvers on Multicore and Manycore CPU Architectures },
author = { Abdullah Alperen and Md Afibuzzaman and Fazlay Rabbi and M. Yusuf \"{O}zkaya and {\"U}mit V. \c{C}ataly\"{u}rek and Hasan Metin Aktulga },
}
@misc { Ozkaya21-GLB,
url = { https://graph-learning-benchmarks.github.io/assets/papers/glb2021/TRIGGER.pdf },
note = { non-archival. },
howpublished = { The Web Conference 2021, Workshop on Graph Learning Benchmarks (GLB 2021) },
month = { Apr },
year = { 2021 },
author = { M. Yusuf \"{O}zkaya and Ali P{\i}nar and {\"U}mit V. \c{C}ataly\"{u}rek },
title = { TRIGGER: TempoRal Interaction Graph GenEratoR },
}
@inproceedings { Gabert21-GrAPL,
doi = { 10.1109/IPDPSW52791.2021.00050 },
organization = { IEEE },
booktitle = { 2021 IEEE International Parallel and Distributed Processing Symposium Workshops (IPDPSW), Workshop on Graphs, Architectures, Programming, and Learning (GrAPL) },
month = { May },
year = { 2021 },
author = { Kasimir Gabert and {\"U}mit V. \c{C}ataly\"{u}rek },
title = { PIGO: A Parallel Graph Input/Output Library },
}
@inproceedings { Gabert21-ParSocial,
doi = { 10.1109/IPDPSW52791.2021.00158 },
organization = { IEEE },
booktitle = { 2021 IEEE International Parallel and Distributed Processing Symposium Workshops (IPDPSW), Workshop on Parallel and Distributed Processing for Computational Social Systems (ParSocial) },
month = { May },
year = { 2021 },
author = { Kasimir Gabert and Ali P{\i}nar and {\"U}mit V. \c{C}ataly\"{u}rek },
title = { Shared-Memory Scalable k-Core Maintenance on Dynamic Graphs and Hypergraphs },
}
@abstract { Yasar21-ICCF,
doi = { 10.1145/3457388.3459987 },
year = { 2021 },
month = { May },
pages = { 212--212 },
howpublished = { Abstract, Proceedings of the 18th ACM International Conference on Computing Frontiers, Big Data Analytics Workshop (BigDAW) },
author = { Abdurrahman Ya\c{s}ar and Kasimir Gabert and {\"U}mit V. \c{C}ataly\"{u}rek },
title = { Parallel graph algorithms by blocks: from I/O to algorithms },
}
@inproceedings { Gabert21-WSDM,
selected = { true },
doi = { 10.1145/3437963.3441790 },
series = { WSDM \'21 },
location = { Virtual Event, Israel },
numpages = { 9 },
pages = { 689–697 },
isbn = { 9781450382977 },
publisher = { ACM },
booktitle = { Proceedings of the 14th ACM International Conference on Web Search and Data Mining (WSDM) },
month = { Mar },
year = { 2021 },
author = { Kasimir Gabert and Ali P{\i}nar and {\"U}mit V. \c{C}ataly\"{u}rek },
title = { A Unifying Framework to Identify Dense Subgraphs on Streams: Graph Nuclei to Hypergraph Cores },
}
@techreport { Yasar20-ARXIV-TC,
url = { http://arxiv.org/abs/2009.12457 },
arxiv = { 2009.12457 },
number = { arXiv:2009.12457 },
month = { Sep },
institution = { ArXiv },
year = { 2020 },
author = { Abdurrahman Ya\c{s}ar and Sivasankaran Rajamanickam and Jonathan W. Berry and {\"U}mit V. \c{C}ataly\"{u}rek },
title = { A Block-Based Triangle Counting Algorithm on Heterogeneous Environments },
}
@techreport { Yasar20-ARXIV-SARMA,
url = { http://arxiv.org/abs/2009.07735 },
arxiv = { 2009.07735 },
number = { arXiv:2009.07735 },
month = { Sep },
institution = { ArXiv },
year = { 2020 },
author = { Abdurrahman Ya\c{s}ar and Muhammed Fatih Bal{\i}n and Xiaojing An and Kaan Sancak and {\"U}mit V. \c{C}ataly\"{u}rek },
title = { On Symmetric Rectilinear Matrix Partitioning },
}
@article { Hein20-TOPC,
year = { 2020 },
number = { 4 },
volume = { 7 },
doi = { 10.1145/3418077 },
journal = { ACM Transactions on Parallel Computing (TOPC) },
author = { Eric Hein and Srinivas Eswar and Abdurrahman Ya\c{s}ar and Jiajia Li and Jeffrey S Young and Thomas M Conte and {\"U}mit V. \c{C}ataly\"{u}rek and Rich Vuduc and Jason Riedy and Bora U\c{c}ar },
title = { Programming strategies for irregular algorithms on the {E}mu {C}hick },
}
@inproceedings { Ozkaya20-GrAPL,
pages = { 227-236 },
organization = { IEEE },
optnote = { GrAPL 2020: Workshop on Graphs, Architectures, Programming, and Learning },
url = { https://ieeexplore.ieee.org/abstract/document/9150480 },
doi = { 10.1109/IPDPSW50202.2020.00051 },
year = { 2020 },
title = { A scalable graph generation algorithm to sample over a given shell distribution },
booktitle = { 2020 IEEE International Parallel and Distributed Processing Symposium Workshops (IPDPSW), Workshop on Graphs, Architectures, Programming, and Learning },
author = { M. Yusuf \"{O}zkaya and Muhammed Fatih Bal{\i}n and Ali P{\i}nar and {\"U}mit V. \c{C}ataly\"{u}rek },
}
@article { Wang19-BMCGenomics,
year = { 2019 },
doi = { 10.1186/s12864-019-6382-x },
volume = { 20 },
journal = { BMC Genomics },
author = { Lingling Wang and Anas Abu-Doleh and Johanna Plank and {\"U}mit V. \c{C}ataly\"{u}rek and Jeffrey Firkins and Zhongtang Yu },
title = { The transcriptome of the rumen ciliate Entodinium caudatum reveals some of its metabolic features },
}
@inproceedings { Afibuzzaman19-HiPC,
year = { 2019 },
month = { Dec },
doi = { 10.1109/HiPC.2019.00052 },
booktitle = { Proceedings of the 26th Annual International Conference on High Performance Computing (HiPC 2019) },
title = { DeepSparse: A Task-parallel Framework for Sparse Solvers on Deep Memory Architectures },
author = { Md Afibuzzaman and Fazlay Rabbi and M. Yusuf \"{O}zkaya and Hasan Metin Aktulga and {\"U}mit V. \c{C}ataly\"{u}rek },
}
@inproceedings { Yasar19-HPEC,
optnote = { One of the Graph Challenge Innovation Award winners. },
year = { 2019 },
doi = { 10.1109/HPEC.2019.8916233 },
booktitle = { IEEE High Performance Extreme Computing Conference (HPEC) },
author = { Abdurrahman Ya\c{s}ar and Sivasankaran Rajamanickam and Jonathan W. Berry and Michael M. Wolf and Jeffrey Young and {\"U}mit V. \c{C}ataly\"{u}rek },
title = { Linear Algebra-Based Triangle Counting via Fine-Grained Tasking on Heterogeneous Environments },
}
@techreport { Yasar19-ARXIV,
url = { https://arxiv.org/abs/1909.12209 },
arxiv = { 1909.12209 },
number = { arXiv:1909.12209 },
month = { Oct },
institution = { ArXiv },
year = { 2019 },
author = { Abdurrahman Ya\c{s}ar and {\"U}mit V. \c{C}ataly\"{u}rek },
title = { Heuristics for Symmetric Rectilinear Matrix Partitioning },
}
@inproceedings { Acer19-HPEC,
organization = { IEEE },
optnote = { One of the Graph Challenge Innovation Award winners. },
year = { 2019 },
doi = { 10.1109/HPEC.2019.8916302 },
booktitle = { High Performance Extreme Computing Conference (HPEC), 2019 IEEE },
author = { Seher Acer and Abdurrahman Ya\c{s}ar and Sivasankaran Rajamanickam and Michael M. Wolf and {\"U}mit V. \c{C}ataly\"{u}rek },
title = { Scalable Triangle Counting on Distributed-Memory Systems },
}
@article { Scheider19-BIONF,
url = { http://oup.prod.sis.lan/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btz646/29171171/btz646.pdf },
doi = { 10.1093/bioinformatics/btz646 },
issn = { 1367-4803 },
abstract = { {In exploring the epidemiology of infectious diseases, networks have been used to reconstruct contacts among individuals and/or populations. Summarizing networks using pathogen metadata (e.g., host species and place of isolation) and a phylogenetic tree is a nascent, alternative approach. In this paper, we introduce a tool for reconstructing transmission networks in arbitrary space from phylogenetic information and metadata. Our goals are to provide a means of deriving new insights and infection control strategies based on the dynamics of the pathogen lineages derived from networks and centrality metrics. We created a web-based application, called StrainHub, in which a user can input a phylogenetic tree based on genetic or other data along with characters derived from metadata using their preferred tree search method. StrainHub generates a transmission network based on character state changes in metadata, such as place or source of isolation, mapped on the phylogenetic tree. The user has the option to calculate centrality metrics on the nodes including betweenness, closeness, degree, and a new metric, the source/hub ratio. The outputs include the network with values for metrics on its nodes and the tree with characters reconstructed. All of these results can be exported for further analysis.strainhub.io and https://github.com/abschneider/StrainHub} },
month = { 08 },
year = { 2019 },
journal = { Bioinformatics },
title = { {StrainHub: A phylogenetic tool to construct pathogen transmission networks} },
author = { Adriano de Bernardi Schneider and Colby T Ford and Reilly Hostager and John Williams and Michael Cioce and {\"U}mit V. \c{C}ataly\"{u}rek and Joel O. Wertheim and Daniel Janies },
}
@article { Deveci19-TPDS,
selected = { true },
doi = { 10.1109/TPDS.2019.2900043 },
pages = { 2018-2032 },
number = { 9 },
volume = { 30 },
year = { 2019 },
journal = { IEEE Transactions on Parallel and Distributed Systems },
title = { Geometric Mapping of Tasks to Processors on Parallel Computers with Mesh or Torus Networks },
author = { Mehmet Deveci and Karen D. Devine and Kevin Pedretti and Mark A. Taylor and Sivasankaran Rajamanickam and {\"U}mit V. \c{C}ataly\"{u}rek },
}
@article { Herrmann19-SISC,
selected = { true },
doi = { 10.1137/18M1176865 },
pages = { A2117-A2145 },
number = { 4 },
volume = { 41 },
year = { 2019 },
optkeywords = { directed graph ; acyclic partitioning ; multilevel partitioning },
journal = { {SIAM} Journal on Scientific Computing (SISC) },
title = { Multilevel Algorithms for Acyclic Partitioning of Directed Acyclic Graphs },
author = { Julien Herrmann and M. Yusuf \"{O}zkaya and Bora U\c{c}ar and Kamer Kaya and {\"U}mit V. \c{C}ataly\"{u}rek },
}
@inproceedings { Ozkaya19-PPAM,
organization = { Springer },
year = { 2019 },
pages = { 211--223 },
month = { Sep },
doi = { 10.1007/978-3-030-43229-4_19 },
booktitle = { Proc. of the 13th International Conf. on Parallel Processing and Applied Mathematics (PPAM) },
title = { Improving Locality-Aware Scheduling with Acyclic Directed Graph Partitioning },
author = { M. Yusuf \"{O}zkaya and Anne Benoit and {\"U}mit V. \c{C}ataly\"{u}rek },
}
@inproceedings { Li19-ICS,
optkeywords = { HiCOO, hierarchical coordinate, reordering, sparse tensor, tensor decomposition },
address = { New York, NY, USA },
publisher = { ACM },
acmid = { 3330366 },
doi = { 10.1145/3330345.3330366 },
numpages = { 11 },
pages = { 227--237 },
location = { Phoenix, Arizona },
isbn = { 978-1-4503-6079-1 },
year = { 2019 },
series = { ICS \'19 },
booktitle = { Proceedings of the ACM International Conference on Supercomputing (ICS) },
title = { Efficient and Effective Sparse Tensor Reordering },
author = { Jiajia Li and Bora U\c{c}ar and {\"U}mit V. \c{C}ataly\"{u}rek and Jimeng Sun and Kevin Barker and Richard Vuduc },
}
@inproceedings { Ozkaya19-IPDPS,
organization = { IEEE },
year = { 2019 },
pages = { 155--165 },
doi = { 10.1109/IPDPS.2019.00026 },
booktitle = { 2019 IEEE International Parallel and Distributed Processing Symposium (IPDPS) },
title = { A scalable clustering-based task scheduler for homogeneous processors using DAG partitioning },
author = { M. Yusuf \"{O}zkaya and Anne Benoit and Bora U\c{c}ar and Julien Herrmann and {\"U}mit V. \c{C}ataly\"{u}rek },
}
@inproceedings { Yasar18-HPEC,
optnote = { One of the Graph Challenge Champions. },
organization = { IEEE },
doi = { 10.1109/HPEC.2018.8547563 },
url = { http://ieeexplore.ieee.org/document/8547563 },
year = { 2018 },
pages = { 1--7 },
booktitle = { High Performance Extreme Computing Conference (HPEC), 2018 IEEE },
author = { Abdurrahman Ya\c{s}ar and Sivasankaran Rajamanickam and Michael M. Wolf and Jonathan W. Berry and {\"U}mit V. \c{C}ataly\"{u}rek },
title = { Fast Triangle Counting Using Cilk },
}
@inproceedings { Yasar18-ASONAM,
year = { 2018 },
month = { Aug },
doi = { 10.1109/ASONAM.2018.8508468 },
booktitle = { IEEE/ACM International Conference on Advances in Social Networks Analysis and Mining (ASONAM) },
title = { SiNA: A Scalable Iterative Network Aligner },
author = { Abdurrahman Ya\c{s}ar and Bora U\c{c}ar and {\"U}mit V. \c{C}ataly\"{u}rek },
}
@inproceedings { Ozkaya18-ASONAM,
optnote = { Extended version is available at {ArXiv}. },
arxiv = { 1711.10634 },
year = { 2018 },
month = { Aug },
doi = { 10.1109/ASONAM.2018.8508323 },
booktitle = { IEEE/ACM International Conference on Advances in Social Networks Analysis and Mining (ASONAM) },
title = { Local Detection of Critical Nodes in Active Networks },
author = { M. Yusuf \"{O}zkaya and Ahmet Erdem Sar{\i}y\"{u}ce and Ali P{\i}nar and {\"U}mit V. \c{C}ataly\"{u}rek },
}
@inproceedings { Yasar2018-KDD,
selected = { true },
arxiv = { 1803.03882 },
optnote = { Also available as a Tech Rep on {ArXiv}. },
url = { http://www.kdd.org/kdd2018/accepted-papers/view/an-iterative-global-structure-assisted-labeled-network-aligner },
year = { 2018 },
doi = { 10.1145/3219819.3220079 },
month = { Aug },
booktitle = { Proceedings of the 24th ACM SIGKDD International Conference on Knowledge Discovery and Data Mining },
title = { An Iterative Global Structure-Assisted Labeled Network Aligner },
author = { Abdurrahman Ya\c{s}ar and {\"U}mit V. \c{C}ataly\"{u}rek },
}
@inproceedings { Hong18-HPDC,
url = { https://dl.acm.org/citation.cfm?id=3208062 },
year = { 2018 },
month = { June },
doi = { 10.1145/3208040.3208062 },
booktitle = { Proc. 27th International Symposium on High-Performance Parallel and Distributed Computing (HPDC) },
title = { Efficient Sparse-Matrix Multi-Vector Product on GPUs },
author = { Changwan Hong and Aravind Sukumaran-Rajam and Bortik Bandyopadhyay and Jinsung Kim and S\"{u}reyya Emre Kurt and Israt Nisa and Shivani Sabhlok and {\"U}mit V. \c{C}ataly\"{u}rek and Srinivasan Parthasarathy and P. Sadayappan },
}
@article { Senturk18-FGCS,
month = { Jan },
number = { 1 },
volume = { 78 },
year = { 2018 },
doi = { 10.1016/j.future.2016.06.008 },
journal = { The Future Generation Computer Systems Journal },
title = { A Resource Provisioning Framework for Bioinformatics Applications in Multi-Cloud Environments },
author = { Izzet F. Senturk and P.Balakrishnan and Anas Abu-Doleh and Kamer Kaya and Qutaibah Malluhi and {\"U}mit V. \c{C}ataly\"{u}rek },
}
@techreport { Herrmann18-HAL,
pdf = { https://hal.inria.fr/hal-01744603/file/RR-9163.pdf },
optkeywords = { directed graph ; acyclic partitioning ; multilevel partitioning ; partitionnement acyclic ; partitionnement multiniveau ; graphes orient{\\'e}s },
month = { Mar },
year = { 2018 },
institution = { {Inria - Research Centre Grenoble -- Rh{\^o}ne-Alpes} },
number = { RR-9163 },
url = { https://hal.inria.fr/hal-01744603 },
author = { Julien Herrmann and M. Yusuf \"{O}zkaya and Bora U{\c c}ar and Kamer Kaya and {\"U}mit V. \c{C}ataly\"{u}rek },
title = { {Acyclic partitioning of large directed acyclic graphs} },
}
@techreport { Ozkaya17-arXiv,
url = { http://arxiv.org/abs/1711.10634 },
arxiv = { 1711.10634 },
number = { arXiv:1711.10634 },
month = { Nov },
year = { 2017 },
author = { M. Yusuf \"{O}zkaya and Ahmet Erdem Sar{\i}y\"{u}ce and {\"U}mit V. \c{C}ataly\"{u}rek and Ali P{\i}nar },
institution = { ArXiv },
title = { Active Betweenness Cardinality: Algorithms and Applications },
}
@inproceedings { Herrmann17-CCGrid,
year = { 2017 },
month = { May },
booktitle = { Proc. of the 17th IEEE/ACM International Symposium on Cluster, Cloud and Grid Computing (CCGrid) },
author = { Julien Herrmann and Jonathan Kho and Bora U\c{c}ar and Kamer Kaya and {\"U}mit V. \c{C}ataly\"{u}rek },
title = { Acyclic Partitioning of Large-Scale Directed Acyclic Graphs },
}
@article { Sariyuce17-TKDD,
year = { 2017 },
volume = { 11 },
pages = { 26:1--26:25 },
doi = { 10.1145/3022668 },
number = { 3 },
month = { Apr },
journal = { ACM Transactions on Knowledge Discovery from Data },
author = { Ahmet Erdem Sar{\i}y\"{u}ce and Kamer Kaya and Erik Saule and {\"U}mit V. \c{C}ataly\"{u}rek },
title = { Graph Manipulations for Fast Centrality Computation },
}
@article { Sariyuce17-TWEB,
selected = { true },
year = { 2017 },
url = { https://dl.acm.org/citation.cfm?id=3057742 },
pages = { 26:1--26:25 },
doi = { 10.1145/3022668 },
number = { 3 },
volume = { 11 },
month = { Jul },
journal = { ACM Transactions on the Web },
author = { Ahmet Erdem Sar{\i}y\"{u}ce and C. Seshadhri and Ali P{\i}nar and {\"U}mit V. \c{C}ataly\"{u}rek },
title = { Nucleus Decompositions for Identifying Hierarchy of Dense Subgraphs },
}
@poster { Johnson16-ISCB,
year = { 2016 },
title = { Identification of key mutation signatures from conservation analysis of gene-pseudogene families in human },
month = { Jul },
doi = { 10.7490/f1000research.1112733.1 },
howpublished = { Poster, journalF1000Research (ISCB Comm J) (ISMB\'16) },
author = { Travis Johnson and Jonathan Kho and {\"U}mit V. \c{C}ataly\"{u}rek and Kun Huang and Yan Zhang },
}
@article { Hoffmann16-JID,
year = { 2016 },
volume = { 213 },
title = { Tracing Origins of the Salmonella Bareilly strain causing a Foodborne Outbreak in the United States },
pages = { 502-508 },
number = { 4 },
month = { Apr },
url = { http://jid.oxfordjournals.org/content/213/4/502.abstract },
journal = { Journal of Infectious Diseases },
doi = { 10.1093/infdis/jiv297 },
author = { Maria Hoffmann and Yan Luo and Steven R. Monday and Narjol Gonzales-Escalona and Andrea R. Ottesen and Tim Muruvanda and Charles Wang and George Kastanis and Christine Keys and Daniel Janies and Izzet F. Senturk and {\"U}mit V. \c{C}ataly\"{u}rek and Hua Wang and Thomas S. Hammack and William J. Wolfgang and Dianna Schoonmaker-Bopp and Alvina Chu and Robert Myers and Julie Haendiges and Peter S. Evans and Jianghong Meng and Errol A. Strain and Marc W. Allard and Eric W. Brown },
}
@article { Deveci16-TPDS,
year = { 2016 },
volume = { 27 },
title = { Multi-jagged: A Scalable Parallel Spatial Partitioning Algorithm },
pages = { 803-817 },
number = { 3 },
month = { Mar },
doi = { 10.1109/TPDS.2015.2412545 },
journal = { IEEE Transactions on Parallel and Distributed Systems },
author = { Mehmet Deveci and Sivasankaran Rajamanickam and Karen D. Devine and {\"U}mit V. \c{C}ataly\"{u}rek },
}
@article { Sariyuce16-DAMI,
year = { 2016 },
volume = { 30 },
pages = { 819--847 },
number = { 4 },
doi = { 10.1007/s10618-015-0440-z },
journal = { Data Mining and Knowledge Discovery (DAMI) },
author = { Ahmet Erdem Sar{\i}y\"{u}ce and Bugra Gedik and Gabriela Jacques-Silva and Kun-Lung Wu and {\"U}mit V. \c{C}ataly\"{u}rek },
title = { SONIC: Streaming Overlapping Community Detection },
}
@article { Sariyuce16-VLDBJ,
year = { 2016 },
volume = { 25 },
pages = { 425--447 },
number = { 3 },
url = { http://link.springer.com/article/10.1007/s00778-016-0423-8 },
journal = { The VLDB Journal },
author = { Ahmet Erdem Sar{\i}y\"{u}ce and Bugra Gedik and Gabriela Jacques-Silva and Kun-Lung Wu and {\"U}mit V. \c{C}ataly\"{u}rek },
title = { Incremental k-core Decomposition: Algorithms and Evaluation },
}
@article { Dytrych16-CRC,
year = { 2016 },
volume = { 207 },
title = { Efficacy of the SU(3) scheme for ab initio large-scale calculations beyond the lightest nuclei },
pages = { 202 - 210 },
url = { http://www.sciencedirect.com/science/article/pii/S0010465516301680 },
journal = { Computer Physics Communications },
author = { T. Dytrych and P. Maris and K. D. Launey and J. P. Draayer and James P. Vary and D. Langr and Erik Saule and M. A. Caprio and {\"U}mit V. \c{C}ataly\"{u}rek and M. Sosonkina },
}
@phdthesis { AbuDoleh16-PhD,
year = { 2016 },
title = { High Performance and Scalable Matching and Assembly of Biological Sequences },
month = { May },
key = { AbuDoleh16-PhD },
institution = { The Ohio State University, Electrical and Computer Engineering },
author = { Anas Abu-Doleh },
}
@phdthesis { Sariyuce15-PhD,
year = { 2015 },
month = { May },
key = { Sariyuce15-PhD },
institution = { The Ohio State University, Computer Science and Engineering },
author = { Ahmet Erdem Sar{\i}y\"{u}ce },
title = { Fast Algorithms for Large-Scale Network Analytics },
}
@phdthesis { Deveci15-PhD,
year = { 2015 },
month = { May },
key = { Deveci15-PhD },
institution = { The Ohio State University, Computer Science and Engineering },
author = { Mehmet Deveci },
title = { Load-Balancing and Task Mapping for Exascale Systems },
}
@article { Janies15-Cladistics,
year = { 2015 },
volume = { 31 },
title = { Phylogenetic visualization of the spread of H7 influenza A viruses },
pages = { 679--691 },
number = { 6 },
month = { Dec },
url = { http://onlinelibrary.wiley.com/doi/10.1111/cla.12107/abstract },
journal = { Cladistics },
author = { Daniel A. Janies and Laura W. Pomeroy and Chris Krueger and Yuqi Zhang and Izzet F. Senturk and Kamer Kaya and {\"U}mit V. \c{C}ataly\"{u}rek },
}
@inproceedings { AbuDoleh15-BigData,
year = { 2015 },
title = { Spaler: Spark and GraphX based de novo genome assembler },
month = { Oct },
doi = { 10.1109/BigData.2015.7363853 },
booktitle = { Proc of IEEE Int{\'}l Conference on BigData },
author = { Anas Abu-Doleh and {\"U}mit V. \c{C}ataly\"{u}rek },
}
@inproceedings { Hatem15-BCB,
year = { 2015 },
title = { {MICA: MicroRNA} Integration for Active Module Discovery },
month = { Sep },
doi = { 10.1145/2808719.2808733 },
booktitle = { Proc. of 6th ACM Conference on Bioinformatics, Computational Biology and Health Informatics (ACM-BCB) },
author = { Ayat Hatem and Kamer Kaya and Jeffrey D. Parvin and Kun Huang and {\"U}mit V. \c{C}ataly\"{u}rek },
}
@article { Sariyuce15-ParCo,
year = { 2015 },
volume = { 47 },
pages = { 3-18 },
month = { Aug },
url = { http://authors.elsevier.com/sd/article/S0167819115000101 },
journal = { Parallel Computing },
author = { Ahmet Erdem Sar{\i}y\"{u}ce and Erik Saule and Kamer Kaya and {\"U}mit V. \c{C}ataly\"{u}rek },
title = { Incremental Closeness Centrality in Distributed Memory },
}
@inproceedings { Janies15-MEDINFO,
year = { 2015 },
title = { Syndromic Surveillance of Infectious Diseases meets Molecular Epidemiology in a Workflow and Phylogeographic Application },
month = { Aug },
doi = { 10.3233/978-1-61499-564-7-766 },
booktitle = { MEDINFO\'15 },
author = { Daniel Janies and Zachary Witter and Christian Gibson and Thomas Kraft and Izzet F. Senturk and {\"U}mit V. \c{C}ataly\"{u}rek },
}
@inproceedings { Sariyuce15-WWW,
year = { 2015 },
arxiv = { 1411.3312 },
note = { Best Paper Award Nominee. },
optnote = { Also available as a Tech Rep on {ArXiv}. Best Paper Award Nominee. },
month = { May },
doi = { 10.1145/2736277.2741640 },
booktitle = { 24th International World Wide Web Conference (WWW) },
author = { Ahmet Erdem Sar{\i}y\"{u}ce and C. Seshadhri and Ali P{\i}nar and {\"U}mit V. \c{C}ataly\"{u}rek },
title = { Finding the Hierarchy of Dense Subgraphs using Nucleus Decompositions },
}
@inproceedings { Deveci15-IPDPS,
year = { 2015 },
title = { Fast and High Quality Topology-Aware Task Mapping },
month = { May },
doi = { 10.1109/IPDPS.2015.93 },
booktitle = { 29th IEEE International Parallel and Distributed Processing Symposium },
author = { Mehmet Deveci and Kamer Kaya and Bora U\c{c}ar and {\"U}mit V. \c{C}ataly\"{u}rek },
}
@article { Deveci15-JPDC,
year = { 2015 },
volume = { 77 },
title = { Hypergraph partitioning for multiple communication cost metrics: Model and methods },
pages = { 69-83 },
month = { Mar },
url = { http://www.sciencedirect.com/science/article/pii/S0743731514002275 },
journal = { Journal of Parallel and Distributed Computing },
doi = { http://dx.doi.org/10.1016/j.jpdc.2014.12.002 },
author = { Mehmet Deveci and Kamer Kaya and Bora U\c{c}ar and {\"U}mit V. \c{C}ataly\"{u}rek },
}
@article { Sariyuce15-JPDC,
year = { 2015 },
volume = { 76 },
pages = { 106-119 },
month = { Feb },
url = { http://www.sciencedirect.com/science/article/pii/S0743731514001282 },
journal = { Journal of Parallel and Distributed Computing },
author = { Ahmet Erdem Sar{\i}y\"{u}ce and Erik Saule and Kamer Kaya and {\"U}mit V. \c{C}ataly\"{u}rek },
title = { Regularizing Graph Centrality Computations },
}
@incollection { Saule15-HDC,
year = { 2015 },
publisher = { Springer },
pages = { 647--667 },
isbn = { ISBN 978-1-4939-2091-4 },
url = { http://link.springer.com/book/10.1007%2F978-1-4939-2092-1 },
editor = { Samee U. Khan and Albert Y. Zomoya },
doi = { 10.1007/978-1-4939-2092-1 },
booktitle = { Handbook on Data Centers },
author = { Erik Saule and Hasan M. Aktulga and Chao Yang and Esmond G. Ng and {\"U}mit V. \c{C}ataly\"{u}rek },
title = { An Out-of-Core Task-based Middleware for Data-Intensive Scientific Computing },
}
@article { Gerber15-IJC,
year = { 2015 },
volume = { 137 },
pages = { 2323--2331 },
number = { 10 },
journal = { International Journal of Cancer },
doi = { 10.1002/ijc.29599 },
author = { Madelyn M. Gerber and Heather Hampel and Xiao-Ping Zhou and Nathan P. Schulz and Adam Suhy and Mehmet Deveci and {\"U}mit V. \c{C}ataly\"{u}rek and Amanda E. Toland },
title = { Allele-specific imbalance mapping at human orthologs of mouse susceptibility to colon cancer (Scc) loci },
}
@article { Ferhatosmanoglu15-IJDMB,
year = { 2015 },
volume = { 13 },
title = { Mitigating Bias in Planning Two-Color Microarray Experiments },
pages = { 31-49 },
number = { 1 },
doi = { 10.1504/IJDMB.2015.070838 },
journal = { International Journal of Data Mining and Bioinformatics },
author = { Nilgun Ferhatosmanoglu and Theodore T. Allen and {\"U}mit V. \c{C}ataly\"{u}rek },
}
@incollection { Deveci15-MiMB,
year = { 2015 },
title = { Querying Co-regulated Genes on Diverse Gene Expression Datasets Via Biclustering },
publisher = { Springer },
editor = { P.H. Guzzi },
doi = { 10.1007/7651_2015_246 },
booktitle = { Methods in Molecular Biology },
author = { Mehmet Deveci and Onur K\"{u}\c{c}\"{u}ktun\c{c} and Kemal Eren and Doruk Bozda\u{g} and Kamer Kaya and {\"U}mit V. \c{C}ataly\"{u}rek },
}
@phdthesis { Hatem14-PhD,
year = { 2014 },
title = { Active Module Discovery: Integrated Approaches of Gene Co-Expression and PPI Networks and MicroRNA Data },
month = { May },
key = { Hatem14-PhD },
institution = { The Ohio State University, Electrical and Computer Engineering },
author = { Ayat Hatem },
}
@article { Kucuktunc14-ACMTIST,
year = { 2014 },
volume = { 5 },
title = { Diversifying Citation Recommendations },
pages = { 55:1-55:21 },
doi = { 10.1145/2668106 },
number = { 4 },
month = { Dec },
journal = { {ACM} Transactions on Intelligent Systems and Technology },
author = { Onur K\"{u}\c{c}\"{u}ktun\c{c} and Erik Saule and Kamer Kaya and {\"U}mit V. \c{C}ataly\"{u}rek },
}
@techreport { Sariyuce14-ARXIV-Nucleus,
year = { 2014 },
arxiv = { 1411.3312 },
number = { arXiv:1411.3312 },
month = { Nov },
institution = { ArXiv },
author = { Ahmet Erdem Sar{\i}y\"{u}ce and C. Seshadhri and Ali P{\i}nar and {\"U}mit V. \c{C}ataly\"{u}rek },
title = { Finding the Hierarchy of Dense Subgraphs using Nucleus Decompositions },
}
@techreport { Sariyuce14-ARXIV,
year = { 2014 },
arxiv = { 1407.6745 },
number = { arXiv:1407.6745 },
month = { Jul },
url = { http://arxiv.org/abs/1407.6745 },
institution = { ArXiv },
author = { Ahmet Erdem Sar{\i}y\"{u}ce and Erik Saule and {\"U}mit V. \c{C}ataly\"{u}rek },
title = { On Distributed Graph Coloring with Iterative Recoloring },
}
@poster { Sariyuce14-NS,
year = { 2014 },
month = { July },
howpublished = { Poster, SIAM Workshop on Network Science (NS14) },
author = { Ahmet Erdem Sar{\i}y\"{u}ce and Erik Saule and Kamer Kaya and {\"U}mit V. \c{C}ataly\"{u}rek },
title = { Computing the Closeness Centrality of Evolving Networks on Clusters },
}
@abstract { Deveci14-CSC,
year = { 2014 },
title = { Partitioning Hypergraphs for Multiple Communication Metrics },
month = { July },
howpublished = { Abstract, The Sixth SIAM Workshop on Combinatorial Scientific Computing (CSC14) },
author = { Mehmet Deveci and Kamer Kaya and Bora U\c{c}ar and {\"U}mit V. \c{C}ataly\"{u}rek },
address = { Lyon, France },
}
@inproceedings { Sariyuce14-MTAAP,
year = { 2014 },
month = { May },
doi = { 10.1109/IPDPSW.2014.156 },
booktitle = { 28th International Parallel and Distributed Processing Symposium Workshops, Workshop on Multithreaded Architectures and Applications (MTAAP) },
author = { Ahmet Erdem Sar{\i}y\"{u}ce and Erik Saule and Kamer Kaya and {\"U}mit V. \c{C}ataly\"{u}rek },
title = { Hardware/Software Vectorization for Closeness Centrality on Multi-/Many-Core Architectures },
}
@inproceedings { Dufosse14-IPDPS,
year = { 2014 },
title = { Randomized matching heuristics with quality guarantees on shared memory parallel computers },
doi = { 10.1109/IPDPS.2014.63 },
month = { May },
booktitle = { 28th IEEE International Parallel and Distributed Processing Symposium },
author = { Fanny Dufoss\\'{e} and Kamer Kaya and Bora U{\c{c}}ar },
}
@inproceedings { Deveci14-IPDPS,
year = { 2014 },
title = { Exploiting Geometric Partitioning in Task Mapping for Parallel Computers },
month = { May },
doi = { 10.1109/IPDPS.2014.15 },
booktitle = { 28th IEEE International Parallel and Distributed Processing Symposium },
author = { Mehmet Deveci and Sivasankaran Rajamanickam and Vitus Leung and Kevin T Pedretti and Stephen L Olivier and David P. Bunde and {\"U}mit V. \c{C}ataly\"{u}rek and Karen D. Devine },
}
@poster { Deveci14-PHDFORUM-IPDPS,
year = { 2014 },
title = { Load Balancing and Task Mapping for Exascale Systems },
note = { PhD Forum award },
month = { May },
howpublished = { Poster, 28th IEEE International Parallel and Distributed Processing Symposium, PHD Forum },
author = { Mehmet Deveci and {\"U}mit V. \c{C}ataly\"{u}rek },
}
@inproceedings { AbuDoleh14-MTAAP,
year = { 2014 },
title = { Extracting Maximal Exact Matches on {GPU} },
month = { May },
doi = { 10.1109/IPDPSW.2014.159 },
booktitle = { 28th International Parallel and Distributed Processing Symposium Workshops, Workshop on Multithreaded Architectures and Applications (MTAAP) },
author = { Anas Abu-Doleh and Kamer Kaya and Mohamed Abouelhoda and {\"U}mit V. \c{C}ataly\"{u}rek },
}
@article { Katian14-CBT,
year = { 2014 },
volume = { 15 },
title = { NUSAP1 influences the DNA damage response by controlling BRCA1 protein levels },
pages = { 533-543 },
number = { 5 },
month = { Feb },
url = { https://www.landesbioscience.com/journals/cbt/article/28019/ },
journal = { Cancer Biology and Therapy },
doi = { 10.4161/cbt.28019 },
author = { Shweta Kotian and Tapahsama Banerjee and Ainsley Lockhart and Kun Huang and {\"U}mit V. \c{C}ataly\"{u}rek and Jeffrey D. Parvin },
}
@inproceedings { Calyam14,
year = { 2014 },
title = { Wide-area overlay networking to manage science DMZ accelerated flows },
pages = { 269-275 },
month = { Feb },
doi = { 10.1109/ICCNC.2014.6785344 },
booktitle = { Computing, Networking and Communications (ICNC), 2014 International Conference on },
author = { P. Calyam and A. Berryman and Erik Saule and H. Subramoni and P. Schopis and G. Springer and {\"U}mit V. \c{C}ataly\"{u}rek and Dhabaleswar K. Panda },
}
@incollection { Kaya14-BKDH,
year = { 2014 },
title = { High-Performance Computing in High-Throughput Sequencing },
publisher = { John Wiley \& Sons },
editor = { Mourad Elloumi and Albert Y. Zomaya },
doi = { 10.1002/9781118617151.ch43 },
booktitle = { Biological Knowledge Discovery Handbook },
author = { Kamer Kaya and Ayat Hatem and Hatice G\"{u}l\c{c}in {\"{O}}zer and Kun Huang and {\"U}mit V. \c{C}ataly\"{u}rek },
}
@article { Jung14-SP,
year = { 2014 },
volume = { 22 },
title = { Exploring the Future of Out-Of-Core Computing with Compute-Local Non-Volatile Memory },
pages = { 125-139 },
number = { 2 },
url = { http://iospress.metapress.com/content/t5805w1557614624/ },
journal = { Scientific Programming },
doi = { 10.3233/SPR-140384 },
author = { Myoungsoo Jung and Ellis H. Wilson III and Wonil Choi and John Shalf and Hasan M. Aktulga and Chao Yang and Erik Saule and {\"U}mit V. \c{C}ataly\"{u}rek and Mahmut Kandemir },
}
@article { Deveci14-BMC,
year = { 2014 },
volume = { 15 },
title = { {mrSNP}: Software to detect {SNP} effects on {microRNA} binding },
pages = { 73 },
url = { http://www.biomedcentral.com/1471-2105/15/73 },
journal = { BMC Bioinformatics },
doi = { 10.1186/1471-2105-15-73 },
author = { Mehmet Deveci and {\"U}mit V. \c{C}ataly\"{u}rek and Amanda E. Toland },
}
@article { Bokhari14,
year = { 2014 },
volume = { 26 },
title = { Massively Multithreaded Maxflow for Image Segmentation on the Cray {XMT-2} },
pages = { 2836-2855 },
number = { 18 },
note = { Also available as a {}technical report from Algopath LLC. },
journal = { Concurrency and Computation: Practice and Experience },
doi = { 10.1002/cpe.3181 },
author = { Shahid H. Bokhari and {\"U}mit V. \c{C}ataly\"{u}rek and Metin N. G\"{u}rcan },
}
@phdthesis { Kucuktunc13-PhD,
year = { 2013 },
title = { Result Diversification on Spatial, Multidimensional, Opinion, and Bibliographic Data },
month = { May },
key = { Kucuktunc13-PhD },
institution = { The Ohio State University, Computer Science and Engineering },
author = { Onur K\"{u}\c{c}\"{u}ktun\c{c} },
}
@article { Dytrych13-PRL,
year = { 2013 },
volume = { 111 },
title = { Collective Modes in Light Nuclei from First Principles },
pages = { 252501 },
number = { 25 },
month = { Dec },
url = { http://link.aps.org/doi/10.1103/PhysRevLett.111.252501 },
journal = { Physical Review Letters },
doi = { 10.1103/PhysRevLett.111.252501 },
author = { T. Dytrych and K. D. Launey and J. P. Draayer and P. Maris and James P. Vary and Erik Saule and {\"U}mit V. \c{C}ataly\"{u}rek and M. Sosonkina and D. Langr and M. A. Caprio },
}
@article { Wang13-PloSONE,
year = { 2013 },
volume = { 8 },
publisher = { Public Library of Science },
pages = { e78507 },
number = { 11 },
month = { Nov },
journal = { PLoS ONE },
doi = { 10.1371/journal.pone.0078507 },
author = { Lingling Wang and Ayat Hatem and {\"U}mit V. \c{C}ataly\"{u}rek and Mark Morrison and Zhongtang Yu },
title = { Metagenomic Insights into the Carbohydrate-Active Enzymes Carried by the Microorganisms Adhering to Solid Digesta in the Rumen of Cows },
}
@inproceedings { Jung13-SC,
year = { 2013 },
title = { Exploring the Future of Out-Of-Core Computing with Compute-Local Non-Volatile Memory },
month = { Nov },
doi = { 10.1145/2503210.2503261 },
booktitle = { Proc. of Conference on High Performance Computing Networking, Storage and Analysis (SC \'13) },
author = { Myoungsoo Jung and Ellis H. Wilson III and Wonil Choi and John Shalf and Hasan M. Aktulga and Chao Yang and Erik Saule and {\"U}mit V. \c{C}ataly\"{u}rek and Mahmut Kandemir },
}
@inproceedings { Sariyuce13-BigData,
year = { 2013 },
month = { Oct },
doi = { 10.1109/BigData.2013.6691611 },
booktitle = { Proc of IEEE Int{\'}l Conference on BigData },
author = { Ahmet Erdem Sar{\i}y\"{u}ce and Kamer Kaya and Erik Saule and {\"U}mit V. \c{C}ataly\"{u}rek },
title = { Incremental Algorithms for Closeness Centrality },
}
@inproceedings { deveci13-icpp-matching,
year = { 2013 },
title = { A Push-Relabel-based Maximum Cardinality Bipartite Matching Algorithm on {GPU}s },
month = { Oct },
doi = { 10.1109/ICPP.2013.11 },
booktitle = { Proc. of 42nd Int{\'}l. Conf. on Parallel Processing },
author = { Mehmet Deveci and Kamer Kaya and Bora U\c{c}ar and {\"U}mit V. \c{C}ataly\"{u}rek },
}
@inproceedings { deveci13-icpp-sparsification,
year = { 2013 },
title = { Hypergraph Sparsification and Its Application to Partitioning },
month = { Oct },
doi = { 10.1109/ICPP.2013.29 },
booktitle = { Proc. of 42nd Int{\'}l. Conf. on Parallel Processing },
author = { Mehmet Deveci and Kamer Kaya and {\"U}mit V. \c{C}ataly\"{u}rek },
}
@inproceedings { Saule13-PPAM,
year = { 2013 },
title = { Performance Evaluation of Sparse Matrix Multiplication Kernels on {I}ntel {X}eon {P}hi },
month = { Sep },
doi = { 10.1007/978-3-642-55224-3_52 },
booktitle = { Proc. of the 10th Int{\'}l Conf. on Parallel Processing and Applied Mathematics (PPAM) },
author = { Erik Saule and Kamer Kaya and {\"U}mit V. \c{C}ataly\"{u}rek },
}
@inproceedings { Sariyuce13-Cluster,
year = { 2013 },
month = { Sep },
doi = { 10.1109/CLUSTER.2013.6702680 },
booktitle = { Proc. of IEEE Cluster 2013 },
author = { Ahmet Erdem Sar{\i}y\"{u}ce and Erik Saule and Kamer Kaya and {\"U}mit V. \c{C}ataly\"{u}rek },
title = { {STREAMER}: a Distributed Framework for Incremental Closeness Centrality Computation },
}
@inproceedings { Kaya13-PPAM,
year = { 2013 },
title = { Analysis of Partitioning Models and Metrics in Parallel Sparse Matrix-Vector Multiplication },
month = { Sep },
doi = { 10.1007/978-3-642-55195-6_16 },
booktitle = { Proc. of the 10th Int{\'}l Conf. on Parallel Processing and Applied Mathematics (PPAM) },
author = { Kamer Kaya and Bora U\c{c}ar and {\"U}mit V. \c{C}ataly\"{u}rek },
}
@inproceedings { Hatem13-BCB,
year = { 2013 },
title = { {PRASE}: PageRank-based Active Subnetwork Extraction },
month = { Sep },
doi = { 10.1145/2506583.2506631 },
booktitle = { Proc. of ACM Conference on Bioinformatics, Computational Biology and Biomedical Informatics (BCB) },
author = { Ayat Hatem and Kamer Kaya and {\"U}mit V. \c{C}ataly\"{u}rek },
}
@inproceedings { AbuDoleh13-BCB,
year = { 2013 },
title = { Masher: Mapping Long(er) Reads with Hash-based Genome Indexing on {GPU}s },
month = { Sep },
doi = { 10.1145/2506583.2506641 },
booktitle = { Proc. of ACM Conference on Bioinformatics, Computational Biology and Biomedical Informatics (BCB) },
author = { Anas Abu-Doleh and Erik Saule and Kamer Kaya and {\"U}mit V. \c{C}ataly\"{u}rek },
}
@inproceedings { Sariyuce13-VLDB,
year = { 2013 },
month = { Aug },
url = { http://www.vldb.org/pvldb/vol6/p433-sariyuce.pdf },
doi = { 10.14778/2536336.2536344 },
booktitle = { 39th International Conference on Very Large Data Bases (VLDB) },
author = { Ahmet Erdem Sar{\i}y\"{u}ce and Bugra Gedik and Gabriela Jacques-Silva and Kun-Lung Wu and {\"U}mit V. \c{C}ataly\"{u}rek },
title = { Streaming Algorithms for k-core Decomposition },
}
@inproceedings { Kucuktunc13-ASONAM,
year = { 2013 },
title = { Towards a Personalized, Scalable, and Exploratory Academic Recommendation Service },
month = { Aug },
doi = { 10.1145/2492517.2492605 },
booktitle = { IEEE/ACM International Conference on Advances in Social Networks Analysis and Mining (ASONAM) },
author = { Onur K\"{u}\c{c}\"{u}ktun\c{c} and Erik Saule and Kamer Kaya and {\"U}mit V. \c{C}ataly\"{u}rek },
}
@inproceedings { deveci13-europar,
year = { 2013 },
title = { GPU accelerated maximum cardinality matching algorithms for bipartite graphs },
month = { Aug },
doi = { 10.1007/978-3-642-40047-6_84 },
booktitle = { Proc. of 19th Int{\'}l. Euro-Par Conf. on Parallel Processing },
author = { Mehmet Deveci and Kamer Kaya and Bora U\c{c}ar and {\"U}mit V. \c{C}ataly\"{u}rek },
}
@article { Benoit13-Workflow,
year = { 2013 },
volume = { 45 },
title = { A Survey of Pipelined Workflow Scheduling: Models and Algorithms },
pages = { 50:1-50:36 },
number = { 4 },
month = { Aug },
url = { http://doi.acm.org/10.1145/2501654.2501664 },
journal = { ACM Computing Surveys },
author = { Anne Benoit and {\"U}mit V. \c{C}ataly\"{u}rek and Yves Robert and Erik Saule },
}
@poster { Kucuktunc13-JCDL,
year = { 2013 },
title = { TheAdvisor: A Webservice for Academic Recommendation },
month = { Jul },
doi = { 10.1145/2467696.2467752 },
howpublished = { Poster, ACM/IEEE Joint Conference on Digital Libraries (JCDL 2013) },
author = { Onur K\"{u}\c{c}\"{u}ktun\c{c} and Erik Saule and Kamer Kaya and {\"U}mit V. \c{C}ataly\"{u}rek },
}
@inproceedings { Sariyuce13-SDM,
year = { 2013 },
arxiv = { 1209.6007 },
note = { An extended version is available as a Tech Rep on {}ArXiv. },
month = { May },
doi = { 10.1137/1.9781611972832.76 },
booktitle = { SIAM International Conference on Data Mining (SDM) },
author = { Ahmet Erdem Sar{\i}y\"{u}ce and Erik Saule and Kamer Kaya and {\"U}mit V. \c{C}ataly\"{u}rek },
title = { Shattering and Compressing Networks for Betweenness centrality },
}
@inproceedings { Kucuktunc13-WWW,
year = { 2013 },
title = { Diversified Recommendation on Graphs: Pitfalls, Measures, and Algorithms },
month = { May },
doi = { 10.1145/2488388.2488451 },
booktitle = { 22nd International World Wide Web Conference (WWW) },
author = { Onur K\"{u}\c{c}\"{u}ktun\c{c} and Erik Saule and Kamer Kaya and {\"U}mit V. \c{C}ataly\"{u}rek },
}
@techreport { Catalyurek13-INRIA,
year = { 2013 },
title = { On analysis of partitioning models and metrics in parallel sparse matrix-vector multiplication },
number = { RR-8301 },
month = { May },
url = { http://hal.inria.fr/hal-00821523 },
institution = { Inria, France },
author = { {\"U}mit V. \c{C}ataly\"{u}rek and Kamer Kaya and Bora U\c{c}ar },
}
@inproceedings { Sariyuce13-GPGPU,
year = { 2013 },
month = { Mar },
doi = { 10.1145/2458523.2458531 },
booktitle = { Workshop on General Purpose Processing Using GPUs (GPGPU), in conjunction with ASPLOS },
author = { Ahmet Erdem Sar{\i}y\"{u}ce and Kamer Kaya and Erik Saule and {\"U}mit V. \c{C}ataly\"{u}rek },
title = { Betweenness Centrality on {GPU}s and Heterogeneous Architectures },
}
@techreport { Saule13-ARXIV,
year = { 2013 },
title = { Performance Evaluation of Sparse Matrix Multiplication Kernels on Intel Xeon Phi },
arxiv = { 1302.1078 },
number = { arXiv:1302.1078 },
month = { Feb },
url = { http://arxiv.org/abs/1302.1078 },
institution = { ArXiv },
author = { Erik Saule and Kamer Kaya and {\"U}mit V. \c{C}ataly\"{u}rek },
}
@techreport { Sariyuce13-ARXIV,
year = { 2013 },
arxiv = { 1303.0422 },
number = { arXiv:1303.0422 },
month = { Feb },
institution = { ArXiv },
author = { Ahmet Erdem Sar{\i}y\"{u}ce and Kamer Kaya and Erik Saule and {\"U}mit V. \c{C}ataly\"{u}rek },
title = { Incremental Algorithms for Network Management and Analysis based on Closeness Centrality },
}
@inproceedings { Kucuktunc13-CSTA,
year = { 2013 },
title = { Result Diversification in Automatic Citation Recommendation },
month = { Feb },
booktitle = { iConference Workshop on Computational Scientometrics: Theory and Applications },
author = { Onur K\"{u}\c{c}\"{u}ktun\c{c} and Erik Saule and Kamer Kaya and {\"U}mit V. \c{C}ataly\"{u}rek },
}
@article { Maris13-JoP,
year = { 2013 },
volume = { 454 },
title = { No Core CI calculations for light nuclei with chiral 2- and 3-body forces },
pages = { 012063 },
number = { 1 },
url = { http://stacks.iop.org/1742-6596/454/i=1/a=012063 },
journal = { Journal of Physics: Conference Series },
author = { Pieter Maris and Hasan M. Aktulga and Sven Binder and Angelo Calci and {\"U}mit V. \c{C}ataly\"{u}rek and Joachim Langhammer and Esmond G. Ng and Erik Saule and Robert Roth and James P. Vary and Chao Yang },
}
@article { Kaya13-COR,
year = { 2013 },
volume = { 40 },
title = { Push-relabel based Algorithms for the Maximum Transversal Problem },
pages = { 1266--1275 },
number = { 5 },
doi = { 10.1016/j.cor.2012.12.009 },
journal = { Computers \& Operations Research },
author = { Kamer Kaya and Johannes Langguth and Fredrik Manne and Bora U\c{c}ar },
}
@article { Kaya13-SIMAX,
year = { 2013 },
volume = { 34 },
title = { Constructing Elimination Trees for Sparse Unsymmetric Matrices },
pages = { 345--354 },
number = { 2 },
doi = { 10.1137/110825443 },
journal = { SIAM Journal on Matrix Analysis and Applications },
author = { Kamer Kaya and Bora U{\c{c}}ar },
}
@article { Kucuktunc13-SNAM,
year = { 2013 },
volume = { 3 },
title = { Fast Recommendation on Bibliographic Networks with Sparse-Matrix Ordering and Partitioning },
pages = { 1097-1111 },
number = { 4 },
url = { http://link.springer.com/article/10.1007%2Fs13278-013-0106-z },
journal = { Social Network Analysis and Mining (SNAM) },
author = { Onur K\"{u}\c{c}\"{u}ktun\c{c} and Kamer Kaya and Erik Saule and {\"U}mit V. \c{C}ataly\"{u}rek },
}
@article { Hatem13-BMC,
year = { 2013 },
volume = { 14 },
title = { Benchmarking Short Sequence Mapping Tools },
number = { 1 },
url = { http://www.biomedcentral.com/1471-2105/14/184 },
journal = { BMC Bioinformatics },
author = { Ayat Hatem and Doruk Bozda\u{g} and Amanda E. Toland and {\"U}mit V. \c{C}ataly\"{u}rek },
}
@article { Eren13-BIB,
year = { 2013 },
volume = { 14 },
title = { A Comparative Analysis of Biclustering Algorithms for Gene Expression Data },
pages = { 279-292 },
number = { 3 },
url = { http://bib.oxfordjournals.org/content/14/3/279 },
journal = { Briefings in Bioinformatics },
author = { Kemal Eren and Mehmet Deveci and Onur K\"{u}\c{c}\"{u}ktun\c{c} and {\"U}mit V. \c{C}ataly\"{u}rek },
}
@article { Duff13-ETNA,
year = { 2013 },
title = { Preconditioners based on Strong Subgraphs },
journal = { Electronic Transactions on Numerical Analysis },
author = { Iain S. Duff and Kamer Kaya },
}
@inproceedings { Hatem12-BCB,
year = { 2012 },
title = { Microarray vs. RNA-Seq: A comparison for active subnetwork discovery },
month = { Oct },
doi = { 10.1145/2382936.2382994 },
booktitle = { {ACM} Conference on Bioinformatics, Computational Biology and Biomedicine (BCB) },
author = { Ayat Hatem and Kamer Kaya and {\"U}mit V. \c{C}ataly\"{u}rek },
}
@article { Catalyurek12-ParCo,
year = { 2012 },
volume = { 38 },
title = { Graph Coloring Algorithms for Multi-core and Massively Multithreaded Architectures },
pages = { 576--594 },
arxiv = { 1205.3809 },
number = { 10-11 },
note = { Also available as an {}arXiv Tech Report. },
month = { Oct-Nov },
doi = { 10.1016/j.parco.2012.07.001 },
journal = { Parallel Computing },
author = { {\"U}mit V. \c{C}ataly\"{u}rek and John Feo and Assefaw H. Gebremedhin and Mahantesh Halappanavar and Alex Pothen },
}
@inproceedings { Zhou12-Cluster,
year = { 2012 },
title = { An Out-of-core Eigensolver on SSD-equipped Clusters },
month = { Sep },
doi = { 10.1109/CLUSTER.2012.76 },
booktitle = { Proc. of IEEE Cluster },
author = { Zheng Zhou and Erik Saule and Hasan M. Aktulga and Chao Yang and Esmond G. Ng and Pieter Maris and James P. Vary and {\"U}mit V. \c{C}ataly\"{u}rek },
}
@inproceedings { Zhou12-P2S2,
year = { 2012 },
title = { An Out-Of-Core Dataflow Middleware to Reduce the Cost of Large Scale Iterative Solvers },
month = { Sep },
doi = { 10.1109/ICPPW.2012.13 },
booktitle = { 2012 International Conference on Parallel Processing (ICPP) Workshops, Fifth International Workshop on Parallel Programming Models and Systems Software for High-End Computing (P2S2) },
author = { Zheng Zhou and Erik Saule and Hasan M. Aktulga and Chao Yang and Esmond G. Ng and Pieter Maris and James P. Vary and {\"U}mit V. \c{C}ataly\"{u}rek },
}
@techreport { Sariyuce12-ARXIV,
year = { 2012 },
arxiv = { 1209.6007 },
number = { arXiv:1209.6007 },
month = { Sep },
url = { http://arxiv.org/abs/1209.6007 },
institution = { ArXiv },
author = { Ahmet Erdem Sar{\i}y\"{u}ce and Erik Saule and Kamer Kaya and {\"U}mit V. \c{C}ataly\"{u}rek },
title = { Shattering and Compressing Networks for Centrality Analysis },
}
@techreport { Kucuktunc12-ARXIV2,
year = { 2012 },
title = { Diversifying Citation Recommendations },
arxiv = { 1209.5809 },
number = { arXiv:1209.5809 },
month = { Sep },
url = { http://arxiv.org/abs/1209.5809 },
institution = { ArXiv },
author = { Onur K\"{u}\c{c}\"{u}ktun\c{c} and Erik Saule and Kamer Kaya and {\"U}mit V. \c{C}ataly\"{u}rek },
}
@inproceedings { Catalyurek12-ICPP,
year = { 2012 },
title = { On shared-memory parallelization of a sparse matrix scaling algorithm },
month = { Sep },
doi = { 10.1109/ICPP.2012.43 },
booktitle = { 2012 International Conference on Parallel Processing (ICPP) },
author = { {\"U}mit V. \c{C}ataly\"{u}rek and Kamer Kaya and Bora U\c{c}ar },
}
@inproceedings { Kucuktunc12-ASONAM,
year = { 2012 },
title = { Fast Recommendation on Bibliographic Networks },
month = { Aug },
doi = { 10.1109/ASONAM.2012.82 },
booktitle = { IEEE/ACM International Conference on Advances in Social Networks Analysis and Mining (ASONAM) },
author = { Onur K\"{u}\c{c}\"{u}ktun\c{c} and Kamer Kaya and Erik Saule and {\"U}mit V. \c{C}ataly\"{u}rek },
}
@inproceedings { Saule12-MTAAP,
year = { 2012 },
title = { An Early Evaluation of the Scalability of Graph Algorithms on the {I}ntel {MIC} Architecture },
month = { May },
doi = { 10.1109/IPDPSW.2012.204 },
booktitle = { 26th International Parallel and Distributed Processing Symposium, Workshops and PhD Forum (IPDPSW), Workshop on Multithreaded Architectures and Applications (MTAAP) },
author = { Erik Saule and {\"U}mit V. \c{C}ataly\"{u}rek },
}
@inproceedings { Sariyuce12-PCO,
year = { 2012 },
month = { May },
doi = { 10.1109/IPDPSW.2012.216 },
booktitle = { 26th International Parallel and Distributed Processing Symposium, Workshops and PhD Forum (IPDPSW), Workshop on Parallel Computing and Optimization (PCO) },
author = { Ahmet Erdem Sar{\i}y\"{u}ce and Erik Saule and {\"U}mit V. \c{C}ataly\"{u}rek },
title = { Scalable Hybrid Implementation of Graph Coloring using MPI and OpenMP },
}
@inproceedings { Catalyurek12-IPDPS,
year = { 2012 },
title = { Multithreaded Clustering for Multi-level Hypergraph Partitioning },
month = { May },
doi = { 10.1109/IPDPS.2012.81 },
booktitle = { 26th IEEE International Parallel and Distributed Processing Symposium },
author = { {\"U}mit V. \c{C}ataly\"{u}rek and Mehmet Deveci and Kamer Kaya and Bora U\c{c}ar },
}
@article { Saule12-JPDC,
year = { 2012 },
volume = { 72 },
title = { Optimizing the maximum stretch of independent tasks on a cluster : From sequential tasks to moldable tasks },
pages = { 489-503 },
number = { 4 },
month = { Apr },
url = { http://www.sciencedirect.com/science/article/pii/S0743731511002474 },
journal = { Journal of Parallel and Distributed Computing },
author = { Erik Saule and Doruk Bozda\u{g} and {\"U}mit V. \c{C}ataly\"{u}rek },
}
@inproceedings { Kaya12-DNASDM,
year = { 2012 },
month = { Apr },
booktitle = { Workshop on Dynamic Network Analysis (DNA-SDM) },
author = { Kamer Kaya and Erik Saule and Onur K\"{u}\c{c}\"{u}ktun\c{c} and {\"U}mit V. \c{C}ataly\"{u}rek },
title = { Algorithms for Offline Tracking of Connected Components in Large Evolving Networks },
}
@techreport { Kucuktunc12-ARXIV,
year = { 2012 },
arxiv = { 1205.1143 },
number = { arXiv:1205.1143 },
month = { Apr },
url = { http://arxiv.org/abs/1205.1143 },
institution = { ArXiv },
author = { Onur K\"{u}\c{c}\"{u}ktun\c{c} and Erik Saule and Kamer Kaya and {\"U}mit V. \c{C}ataly\"{u}rek },
title = { Recommendation on Academic Networks using Direction Aware Citation Analysis },
}
@article { Jeannot-12-JPDC,
year = { 2012 },
volume = { 72 },
pages = { 268 -- 280 },
number = { 2 },
month = { Feb },
doi = { 10.1016/j.jpdc.2011.11.003 },
journal = { Journal of Parallel and Distributed Computing },
author = { Emmanuel Jeannot and Erik Saule and Denis Trystram },
title = { Optimizing Performance and Reliability on Heterogeneous Parallel Systems: Approximation Algorithms and Heuristics },
}
@inproceedings { Catalyurek13-Cluster,
year = { 2012 },
note = { Published in Contemporary Mathematics, Vol. 588, Editors D.A. Bader, H. Meyerhenke, P. Sanders, D. Wagner, 2013. },
month = { Feb },
booktitle = { 10th DIMACS Implementation Challenge - Graph Partitioning and Graph Clustering },
author = { {\"U}mit V. \c{C}ataly\"{u}rek and Kamer Kaya and Johannes Langguth and Bora U\c{c}ar },
title = { A divisive clustering technique for maximizing the modularity },
}
@inproceedings { Catalyurek13-UMPa,
year = { 2012 },
note = { Published in Contemporary Mathematics, Vol. 588, Editors D.A. Bader, H. Meyerhenke, P. Sanders, D. Wagner, 2013. },
month = { Feb },
booktitle = { 10th DIMACS Implementation Challenge Workshop: Graph Partitioning and Graph Clustering },
author = { {\"U}mit V. \c{C}ataly\"{u}rek and Mehmet Deveci and Kamer Kaya and Bora U\c{c}ar },
title = { UMPa: A multi-objective, multi-level partitioner for communication minimization },
}
@article { Xian12,
year = { 2012 },
volume = { 1 },
publisher = { Springer },
pages = { 103-116 },
number = { 3 },
doi = { 10.1007/s13721-012-0009-3 },
journal = { Network Modeling and Analysis in Health Informatics and Bioinformatics },
author = { Yang Xiang and David Fuhry and Kamer Kaya and Ruoming Jin and {\"U}mit V. \c{C}ataly\"{u}rek and Kun Huang },
title = { Merging network patterns: a general framework to summarize biomedical network data },
}
@article { Teodoro12-CC,
year = { 2012 },
volume = { 15 },
title = { Optimizing dataflow applications on heterogeneous environments },
pages = { 125-144 },
number = { 2 },
doi = { 10.1007/s10586-010-0151-6 },
journal = { Cluster Computing },
author = { George Teodoro and Timothy D. R. Hartley and {\"U}mit V. \c{C}ataly\"{u}rek and Renato Ferreira },
}
@article { Saule12-JPDC-spart,
year = { 2012 },
volume = { 72 },
pages = { 1201-1214 },
number = { 10 },
arxiv = { 1104.2566 },
optnote = { Also available as a {}Tech Rep on arXiv. },
doi = { 10.1016/j.jpdc.2012.05.013 },
journal = { Journal of Parallel and Distributed Computing },
author = { Erik Saule and Erdeniz O. Bas and {\"U}mit V. \c{C}ataly\"{u}rek },
title = { Load-Balancing Spatially Located Computations using Rectangular Partitions },
}
@abstract { Sariyuce12-SIAMPP,
year = { 2012 },
howpublished = { Abstract, SIAM Conference on Parallel Processing for Scientific Computing },
author = { Ahmet Erdem Sar{\i}y\"{u}ce and Erik Saule and {\"U}mit V. \c{C}ataly\"{u}rek },
title = { Considerations on Parallel Graph Coloring Algorithms },
}
@inproceedings { Maris12-HITES,
year = { 2012 },
volume = { 403 },
number = { 012019 },
url = { http://iopscience.iop.org/1742-6596/403/1/012019/ },
doi = { doi:10.1088/1742-6596/403/1/012019 },
booktitle = { Journal of Physics: Conference Series. HITES 2012: \'Horizons of Innovative Theories, Experiments, and Supercomputing in Nuclear Physics\' },
author = { Pieter Maris and Hasan M. Aktulga and Mark A Caprio and {\"U}mit V. \c{C}ataly\"{u}rek and Edmong Ng and Dossay Oryspayev and Hugh Potter and Erik Saule and Masha Sosonkina and James P. Vary and Chao Yang and Zheng Zhou },
title = { Large-scale ab initio configuration interaction calculations for light nuclei },
}
@article { Kayaaslan12-SISC,
year = { 2012 },
volume = { 34 },
title = { Partitioning Hypergraphs in Scientific Computing Applications through Vertex Separators on Graphs },
pages = { A970-A992 },
number = { 2 },
note = { A longer version is also available as a {}Tech Rep. },
url = { http://epubs.siam.org/sisc/resource/1/sjoce3/v34/i2/pA970_s1 },
journal = { {SIAM} Journal on Scientific Computing (SISC) },
author = { Enver Kayaaslan and Ali P{\i}nar and {\"U}mit V. \c{C}ataly\"{u}rek and Cevdet Aykanat },
}
@inproceedings { Kucuktunc12-DBRank,
year = { 2012 },
title = { Direction Awareness in Citation Recommendation },
pages = { 6 },
arxiv = { 1205.1143 },
note = { An extended version is available as a Tech Rep on {}ArXiv. },
booktitle = { Proceedings of the 6th International Workshop on Ranking in Databases (DBRank) },
author = { Onur K\"{u}\c{c}\"{u}ktun\c{c} and Erik Saule and Kamer Kaya and {\"U}mit V. \c{C}ataly\"{u}rek },
}
@article { Hartley12-PARCO,
year = { 2012 },
volume = { 38 },
title = { Improving Performance of Adaptive Component-Based Dataflow Middleware },
pages = { 289-309 },
number = { 6-7 },
doi = { 10.1016/j.parco.2012.03.005 },
journal = { Parallel Computing },
author = { Timothy D. R. Hartley and Erik Saule and {\"U}mit V. \c{C}ataly\"{u}rek },
}
@incollection { Boman12-CSC-Zoltan,
year = { 2012 },
title = { Parallel Partitioning, Coloring, and Ordering for Scientific Computing },
series = { Computational Science },
publisher = { Chapman \& Hall / CRC Press },
editor = { Uwe Naumann and Olaf Schenk },
booktitle = { Combinatorial Scientific Computing },
author = { Erik G. Boman, {\"U}mit V. \c{C}ataly\"{u}rek and Cedric Chevalier and Karen D. Devine },
}
@article { Boman12-SciProg,
year = { 2012 },
volume = { 20 },
title = { The Zoltan and Isorropia parallel toolkits for combinatorial scientific computing: Partitioning, ordering and coloring },
pages = { 129-150 },
number = { 2 },
url = { http://iospress.metapress.com/content/U40KU26NRQKP1318 },
journal = { Scientific Programming },
author = { Erik G. Boman and {\"U}mit V. \c{C}ataly\"{u}rek and Cedric Chevalier and Karen D. Devine },
}
@incollection { Bisseling12-CSC-2D,
year = { 2012 },
title = { Two-dimensional approaches to sparse matrix partitioning },
series = { Computational Science },
publisher = { Chapman \& Hall / CRC Press },
editor = { Uwe Naumann and Olaf Schenk },
booktitle = { Combinatorial Scientific Computing },
author = { Rob H. Bisseling and Bas O. Fagginger Auer and A.N. Yzelman and Tristan van Leeuwen and {\"U}mit V. \c{C}ataly\"{u}rek },
}
@abstract { Bas12-SIAMPP,
year = { 2012 },
title = { Load-Balancing Spatially Located Computations using Rectangular Partitions },
doi = { 10.1016/j.jpdc.2012.05.013 },
howpublished = { Abstract, SIAM Conference on Parallel Processing for Scientific Computing },
author = { Erdeniz O. Bas and Erik Saule and {\"U}mit V. \c{C}ataly\"{u}rek },
}
@phdthesis { Hartley11-PhD,
year = { 2011 },
title = { Accelerating Component-Based Dataflow Middleware with Adaptivity and Heterogeneity },
month = { May },
key = { Hartley11-PhD },
institution = { The Ohio State University, Electrical and Computer Engineering },
author = { Timothy D. R. Hartley },
}
@inproceedings { Sariyuce11-HiPC,
year = { 2011 },
month = { Dec },
doi = { 10.1109/HiPC.2011.6152726 },
booktitle = { Proceedings of the 18th Annual International Conference on High Performance Computing (HiPC 2011) },
author = { Ahmet Erdem Sar{\i}y\"{u}ce and Erik Saule and {\"U}mit V. \c{C}ataly\"{u}rek },
title = { Improving Graph Coloring on Distributed Memory Parallel Computers },
}
@inproceedings { Hatem11-BIBM,
year = { 2011 },
title = { Benchmarking Short Sequence Mapping Tools },
note = { A longer version is also available as a {}Tech Rep. },
month = { Nov },
doi = { 10.1109/BIBM.2011.83 },
booktitle = { IEEE International Conference on Bioinformatics and Biomedicine (BIBM11) },
author = { Ayat Hatem and Doruk Bozda\u{g} and {\"U}mit V. \c{C}ataly\"{u}rek },
}
@article { Vydyanathan11-PC,
year = { 2011 },
volume = { 37 },
title = { Optimizing Latency and Throughput of Application Workflows on Clusters },
pages = { 694-712 },
number = { 10-11 },
month = { Oct-Nov },
doi = { 10.1016/j.parco.2010.05.003 },
journal = { Parallel Computing },
author = { Nagavijayalakshmi Vydyanathan and {\"U}mit V. \c{C}ataly\"{u}rek and Tahsin M. Kurc and P. Sadayappan and Joel H. Saltz },
}
@inproceedings { Cooper11-HISB,
year = { 2011 },
title = { Acceleration of Point Correlation Function Calculation for Pathology Image Segmentation },
month = { Jul },
doi = { 10.1109/HISB.2011.10 },
booktitle = { Proceedings of the IEEE Health Informatics and Systems Biology Conference },
author = { Lee Cooper and Joel H. Saltz and {\"U}mit V. \c{C}ataly\"{u}rek and Kun Huang },
}
@inproceedings { Catalyurek11-DIDC,
year = { 2011 },
title = { Integrated Data Placement and Task Assignment for Scientific Workflows in Clouds },
month = { Jun },
doi = { 10.1145/1996014.1996022 },
booktitle = { The Fourth International Workshop on Data Intensive Distributed Computing (DIDC 2011), in conjunction with the 20th International Symposium on High Performance Distributed Computing (HPDC 2011) },
author = { {\"U}mit V. \c{C}ataly\"{u}rek and Kamer Kaya and Bora U\c{c}ar },
}
@article { Janies11-Supramap,
year = { 2011 },
volume = { 27 },
title = { The Supramap project: Linking pathogen genomes with geography to fight emergent infectious diseases },
pages = { 61-66 },
number = { 1 },
month = { Feb },
url = { http://onlinelibrary.wiley.com/doi/10.1111/j.1096-0031.2010.00314.x/abstract },
journal = { Cladistics },
author = { D. A. Janies and T. Treseder and B. Alexandrov and F. Habib and J. J. Chen and R. Ferreira and {\"U}mit V. \c{C}ataly\"{u}rek and A. Varon and W. C. Wheeler },
}
@article { Catalyurek11-Order,
pdf = { Catalyurek11-Order.pdf },
year = { 2011 },
volume = { 33 },
title = { Hypergraph Partitioning-Based Fill-Reducing Ordering },
pages = { 1996-2023 },
number = { 4 },
month = { Feb },
doi = { 10.1137/090757575 },
journal = { {SIAM} Journal on Scientific Computing (SISC) },
author = { {\"U}mit V. \c{C}ataly\"{u}rek and Cevdet Aykanat and Enver Kayaaslan },
}
@article { Vieland11-KELVIN,
year = { 2011 },
volume = { 72 },
title = { KELVIN: a Software Package for Rigorous Measurement of Statistical Evidence in Human Genetics },
pages = { 276-288 },
number = { 5 },
url = { http://www.ncbi.nlm.nih.gov/pubmed/22189470 },
journal = { Human Heredity },
author = { V.J. Vieland and Y. Huang and S.C. Seok and J. Burian and {\"U}mit V. \c{C}ataly\"{u}rek and J. O{\'}Connell and A. Segre and W. Valentine-Cooper },
}
@inproceedings { Saule11-IPDPS,
year = { 2011 },
title = { Partitioning Spatially Located Computations using Rectangles },
doi = { 10.1109/IPDPS.2011.72 },
booktitle = { 25th IEEE International Parallel and Distributed Processing Symposium },
author = { Erik Saule and Erdeniz O. Bas and {\"U}mit V. \c{C}ataly\"{u}rek },
}
@article { Igual11,
year = { 2011 },
volume = { 25 },
title = { Color and Texture Analysis on Emerging Architectures Parallel Architectures },
pages = { 404-427 },
number = { 4 },
url = { http://hpc.sagepub.com/content/early/2010/12/21/1094342010390340 },
journal = { International Journal of High Performance Computing Applications },
author = { F. Igual and R. Mayo and Timothy D. R. Hartley and {\"U}mit V. \c{C}ataly\"{u}rek and Antonio Ruiz and M. Ujaldon },
}
@poster { Deveci11-BCB,
year = { 2011 },
title = { A comparison of recent biclustering algorithms },
note = { Runner-up of the poster award },
howpublished = { Poster, {ACM} International Conference on Bioinformatics and Computational Biology },
author = { Mehmet Deveci and Kemal Eren and {\"U}mit V. \c{C}ataly\"{u}rek },
}
@inproceedings { Aktulga11-HPSS,
year = { 2011 },
title = { On Reducing I/O Overheads in Large-Scale Invariant Subspace Projections },
doi = { 10.1007/978-3-642-29737-3_35 },
booktitle = { Workshop on Algorithms and Programming Tools for Next-Generation High-Performance Scientific Software (HPSS 2011), in conjunction with the Euro-Par },
author = { Hasan M. Aktulga and C. Yang and {\"U}mit V. \c{C}ataly\"{u}rek and P. Maris and James P. Vary and E. G. Ng },
}
@incollection { Catalyurek11-EPC-HP,
year = { 2011 },
title = { Hypergraph Partitioning },
publisher = { Springer },
pages = { 871-881 },
url = { http://www.springerlink.com/content/v2124348m4nkh635/ },
editor = { David Padua },
booktitle = { Encyclopedia of Parallel Computing },
author = { {\"U}mit V. \c{C}ataly\"{u}rek and Bora U\c{c}ar and Cevdet Aykanat },
}
@incollection { Catalyurek11-EPC-PaToH,
year = { 2011 },
title = { {PaToH} (Partitioning Tool for Hypergraphs) },
publisher = { Springer },
pages = { 1479-1487 },
url = { http://www.springerlink.com/content/g5t6638gm542837t/ },
editor = { David Padua },
booktitle = { Encyclopedia of Parallel Computing },
author = { {\"U}mit V. \c{C}ataly\"{u}rek and Cevdet Aykanat },
}
@inproceedings { Catalyurek11-PCO,
year = { 2011 },
title = { Distributed-Memory Parallel Algorithms for Matching and Coloring },
pages = { 1966-1975 },
doi = { 10.1109/IPDPS.2011.360 },
booktitle = { 2011 International Parallel and Distributed Processing Symposium, Workshops and PhD Forum (IPDPSW), Workshop on Parallel Computing and Optimization (PCO\'11) },
author = { {\"U}mit V. \c{C}ataly\"{u}rek and Florin Dobrian and Assefaw H. Gebremedhin and Mahantesh Halappanavar and Alex Pothen },
}
@phdthesis { Sertel10-PhD,
year = { 2010 },
title = { Image Analysis for Computer-Aided Histopathology },
month = { May },
key = { Sertel10-PhD },
institution = { The Ohio State University, Electrical and Computer Engineering },
author = { Olcay Sertel },
}
@techreport { Benoit10-Workflow,
year = { 2010 },
title = { A Survey of Pipelined Workflow Scheduling: Models and Algorithms },
number = { RR-LIP-2010-28 },
month = { Sep },
url = { http://hal.archives-ouvertes.fr/hal-00521712/fr/ },
institution = { LIP },
author = { Anne Benoit and {\"U}mit V. \c{C}ataly\"{u}rek and Yves Robert and Erik Saule },
address = { ENS Lyon, France },
}
@inproceedings { Sertel10-ICPR,
year = { 2010 },
title = { An Image Analysis Approach for Detecting Malignant Cells in Digitized H amp;E-stained Histology Images of Follicular Lymphoma },
pages = { 273 -276 },
month = { Aug },
doi = { 10.1109/ICPR.2010.76 },
booktitle = { 20th International Conference on Pattern Recognition (ICPR) },
author = { Olcay Sertel and {\"U}mit V. \c{C}ataly\"{u}rek and G. Lozanski and A. Shanaah and Metin N. G\"{u}rcan },
}
@article { Ucar10-ParCo,
pdf = { Ucar10-ParCo.pdf },
year = { 2010 },
volume = { 36 },
title = { A matrix partitioning interface to {PaToH} in {MATLAB} },
pages = { 254 - 272 },
number = { 5-6 },
journal = { Parallel Computing },
doi = { 10.1016/j.parco.2009.12.008 },
author = { Bora U\c{c}ar and {\"U}mit V. \c{C}ataly\"{u}rek and Cevdet Aykanat },
}
@inproceedings { Ucar10-PDP,
pdf = { Ucar10-PDP.pdf },
year = { 2010 },
title = { On scalability of hypergraph models for sparse matrix partitioning },
doi = { 10.1109/PDP.2010.92 },
booktitle = { Proc. of the PDP 2010: 18th Euromicro International Conference on Parallel, Distributed and Network-Based Computing },
author = { Bora U\c{c}ar and {\"U}mit V. \c{C}ataly\"{u}rek },
}
@inproceedings { Teodoro10-HPDC,
year = { 2010 },
title = { Run-time optimizations for replicated dataflows on heterogeneous environments },
pages = { 13--24 },
note = { Best Student Paper Award },
url = { http://portal.acm.org/Graph Based Citation Analysis.cfm?id=1851479 },
booktitle = { Proc. of the 19th ACM International Symposium on High Performance Distributed Computing (HPDC) },
author = { George Teodoro and Timothy D. R. Hartley and {\"U}mit V. \c{C}ataly\"{u}rek and Renato Ferreira },
}
@abstract { Saule10-Aussois,
year = { 2010 },
title = { Optimizing the maximum stretch of online tasks on a parallel system without preemption },
howpublished = { Abstract, 3rd Scheduling in Aussois Workshop },
author = { Erik Saule and Doruk Bozda\u{g} and {\"U}mit V. \c{C}ataly\"{u}rek },
}
@inproceedings { Saule10-JSSPP,
year = { 2010 },
volume = { 6253 },
title = { A Moldable Online Scheduling Algorithm and its Application to Parallel Short Sequence Mapping },
series = { Lecture notes in Computer Science },
publisher = { Springer },
booktitle = { Job Scheduling Strategies for Parallel Processing },
author = { Erik Saule and Doruk Bozda\u{g} and {\"U}mit V. \c{C}ataly\"{u}rek },
}
@abstract { Saule10-NCST,
year = { 2010 },
title = { Partitioning Spatially Located Load with Rectangles: Algorithms and Simulations },
howpublished = { Abstract, New Challenges on Scheduling Theory, Workshop },
author = { Erik Saule and Erdeniz O. Bas and {\"U}mit V. \c{C}ataly\"{u}rek },
}
@abstract { Hatem10-OCCBIO,
year = { 2010 },
title = { Benchmarking Short Sequence Alignment Tools },
howpublished = { Abstract, Bioinformatics, 2010 Ohio Collaborative Conference },
author = { Ayat Hatem and Doruk Bozda\u{g} and {\"U}mit V. \c{C}ataly\"{u}rek },
}
@inproceedings { Hartley10-HiPC,
year = { 2010 },
title = { Automatic Dataflow Application Tuning for Heterogeneous Systems },
booktitle = { Proceedings of The 17th International Conference on High Performance Computing (HiPC 2010) },
author = { Timothy D. R. Hartley and Erik Saule and {\"U}mit V. \c{C}ataly\"{u}rek },
}
@inproceedings { Bozdag10-BCB,
year = { 2010 },
title = { Comparative Analysis of Biclustering Algorithms },
booktitle = { {ACM} International Conference on Bioinformatics and Computational Biology },
author = { Doruk Bozda\u{g} and A.S. Kumar and {\"U}mit V. \c{C}ataly\"{u}rek },
}
@inproceedings { Bozdag10-HiCOMB,
year = { 2010 },
title = { Exploring Parallelism in Short Sequence Mapping Using Burrows-Wheeler Transform },
booktitle = { 9th IEEE International Workshop on High Performance Computational Biology (in conjunction with IPDPS) },
author = { Doruk Bozda\u{g} and Ayat Hatem and {\"U}mit V. \c{C}ataly\"{u}rek },
}
@article { Bozdag10-SISC,
year = { 2010 },
volume = { 32 },
title = { Distributed-memory Parallel Algorithms for Distance-2 Coloring and Related Problems in Derivative Computation },
pages = { 2418-2446 },
number = { 4 },
doi = { 10.1137/080732158 },
journal = { {SIAM} Journal on Scientific Computing (SISC) },
author = { Doruk Bozda\u{g} and {\"U}mit V. \c{C}ataly\"{u}rek and Assefaw H. Gebremedhin and F. Manne and Erik G. Boman and F. {\"{O}}zg\"{u}ner },
}
@article { Catalyurek10-RESS,
year = { 2010 },
volume = { 95 },
title = { Development of a code-agnostic computational infrastructure for the dynamic generation of accident progression even trees },
pages = { 278 - 294 },
number = { 3 },
doi = { 10.1016/j.ress.2009.10.008 },
journal = { Reliability Engineering and System Safety },
author = { {\"U}mit V. \c{C}ataly\"{u}rek and B. Rutt and K. Metzroth and Aram Hakobyan and T. Aldemir and R. Denning and S. Dunagan and D. Kunsman },
}
@incollection { Catalyurek10-SCMA,
year = { 2010 },
title = { Dataflow frameworks for emerging heterogeneous architectures and its application to biomedicine },
publisher = { Chapman and Hall / CRC Press },
editor = { Jack Dongarra and David A. Bader and Jakub Kurzak },
booktitle = { Scientific Computing with Multicore and Accelerators },
author = { {\"U}mit V. \c{C}ataly\"{u}rek and Renato Ferreira and Timothy D. R. Hartley and Rafael Sachetto and George Teodoro },
}
@article { Catalyurek10-SISC,
pdf = { Catalyurek10-SISC.pdf },
year = { 2010 },
volume = { 32 },
publisher = { SIAM },
pages = { 656-683 },
number = { 2 },
doi = { 10.1137/080737770 },
journal = { {SIAM} Journal on Scientific Computing (SISC) },
author = { {\"U}mit V. \c{C}ataly\"{u}rek and Cevdet Aykanat and Bora U\c{c}ar },
title = { On Two-Dimensional Sparse Matrix Partitioning: Models, Methods, and a Recipe },
}
@article { Vydyanathan09-TPDS,
year = { 2009 },
volume = { 20 },
title = { An Integrated Approach to Locality Conscious Processor Allocation and Scheduling of Mixed Parallel Applications },
number = { 8 },
month = { Aug },
doi = { 10.1109/TPDS.2008.219 },
journal = { IEEE Transactions on Parallel and Distributed Systems },
author = { Nagavijayalakshmi Vydyanathan and {\"U}mit V. \c{C}ataly\"{u}rek and Tahsin M. Kurc and P. Sadayappan and Joel H. Saltz },
}
@article { Catalyurek09-JPDC,
year = { 2009 },
doi = { 10.1016/j.jpdc.2009.04.011 },
volume = { 69 },
title = { A Repartitioning Hypergraph Model for Dynamic Load Balancing },
pages = { 711-724 },
number = { 8 },
month = { Aug },
journal = { Journal of Parallel and Distributed Computing },
author = { {\"U}mit V. \c{C}ataly\"{u}rek and Erik G. Boman and K.D. Devine and Doruk Bozda\u{g} and R. Heaphy and L.A. Fisk },
}
@article { Ruiz09-JDMB,
year = { 2009 },
volume = { 3 },
title = { Stroma classification for neuroblastoma on graphics processors },
pages = { 280-298 },
opturl = { http://www.ingentaconnect.com/content/ind/ijdmb/2009/00000003/00000003/art00003 },
month = { Jun },
journal = { International Journal of Data Mining and Bioinformatics },
author = { Antonio Ruiz and Olcay Sertel and Manuel Ujaldon and {\"U}mit V. \c{C}ataly\"{u}rek and Joel H. Saltz and Metin N. G\"{u}rcan },
}
@article { Bozdag09-TPDS,
year = { 2009 },
volume = { 20 },
title = { Compaction of Schedules and a Two-Stage Approach for Duplication-Based {DAG} Scheduling },
pages = { 857-871 },
number = { 6 },
month = { Jun },
url = { http://doi.ieeecomputersociety.org/10.1109/TPDS.2008.260 },
journal = { {IEEE} Transactions on Parallel and Distributed Systems },
author = { Doruk Bozda\u{g} and F. {\"{O}}zg\"{u}ner and {\"U}mit V. \c{C}ataly\"{u}rek },
}
@inproceedings { Hartley09-HCW,
year = { 2009 },
title = { A Component-Based Framework for the Cell Broadband Engine },
month = { May },
booktitle = { Proc. of 23rd Int{\'}l. Parallel and Distributed Processing Symposium, The 18th Heterogeneous Computing Workshop (HCW 2009) },
author = { Timothy D. R. Hartley and {\"U}mit V. \c{C}ataly\"{u}rek },
}
@inproceedings { Bozdag09-IPDPS,
year = { 2009 },
title = { Parallel Short Sequence Mapping for High Throughput Genome Sequencing },
pages = { 1-10 },
month = { May },
booktitle = { Proc. of 23rd Int{\'}l. Parallel and Distributed Processing Symposium },
author = { Doruk Bozda\u{g} and C.C. Barbacioru and {\"U}mit V. \c{C}ataly\"{u}rek },
}
@inproceedings { Teodoro09-Cluster,
year = { 2009 },
title = { Coordinating the Use of {GPU} and {CPU} for Improving Performance of Compute Intensive Applications },
booktitle = { Proc. of the 2009 IEEE International Conference on Cluster Computing },
author = { George Teodoro and Rafael Sachetto and Olcay Sertel and Metin N. G\"{u}rcan and Wagner Meira and {\"U}mit V. \c{C}ataly\"{u}rek and Renato Ferreira },
}
@article { Sertel09-SPS,
year = { 2009 },
volume = { 55 },
title = { Histopathological Image Analysis Using Model-Based Intermediate Representations and Color Texture: Follicular Lymphoma Grading },
pages = { 169-183 },
number = { 1-3 },
doi = { 10.1007/s11265-008-0201-y },
journal = { Signal Processing Systems },
author = { Olcay Sertel and Jun Kong and {\"U}mit V. \c{C}ataly\"{u}rek and Gerard Lozanski and Joel H. Saltz and Metin N. G\"{u}rcan },
}
@article { Sertel09-PatRec,
year = { 2009 },
volume = { 42 },
title = { Computer-aided prognosis of neuroblastoma on whole-slide images: Classification of stromal development },
pages = { 1093-1103 },
number = { 6 },
doi = { 10.1016/j.patcog.2008.08.027 },
journal = { Pattern Recognition },
author = { Olcay Sertel and Jun Kong and H. Shimada and {\"U}mit V. \c{C}ataly\"{u}rek and Joel H. Saltz and Metin N. G\"{u}rcan },
}
@inproceedings { Parvin09-OCCBIO,
year = { 2009 },
title = { Identification of a Breast Cancer Associated Regulatory Network },
publisher = { IEEE Computer Society },
pages = { 71-75 },
url = { http://doi.ieeecomputersociety.org/10.1109/OCCBIO.2009.37 },
booktitle = { Bioinformatics, 2009 Ohio Collaborative Conference },
author = { Jeffrey D. Parvin and Zeina Kais and Mansi Arora and Shweta Kotian and Alicia Zha and Derek Ransburgh and Doruk Bozda\u{g} and {\"U}mit V. \c{C}ataly\"{u}rek and Kun Huang },
address = { Los Alamitos, CA },
}
@inproceedings { Ozer09-BICOB,
year = { 2009 },
volume = { 5462 },
title = { A Comprehensive Analysis Workflow for Genome-Wide Screening Data from ChIP-Sequencing Experiments },
series = { Lecture notes in Computer Science },
publisher = { Springer },
pages = { 320-330 },
doi = { 10.1007/978-3-642-00727-9_30 },
booktitle = { Proc. of 1st Int{\'}l. Conf. on Bioinformatics and Computational Biology },
author = { Hatice G. Ozer and Doruk Bozda\u{g} and T. Camerlengo and J. Wu and Y.-W. Huang and Timothy D. R. Hartley and Jeffrey D. Parvin and T. Huang and {\"U}mit V. \c{C}ataly\"{u}rek and K. Huang },
}
@inproceedings { igual09parco,
year = { 2009 },
title = { Exploring the {GPU} for Enhancing Parallelism on Color and Texture Analysis },
booktitle = { Proc. of the 2009 International Conference on Parallel Computing (ParCo2009) },
author = { Francisco Igual and Rafael Mayo and Timothy D. R. Hartley and {\"U}mit V. \c{C}ataly\"{u}rek and Antonio Ruiz and Manuel Ujaldon },
}
@inproceedings { Hartley09-PPAC,
year = { 2009 },
title = { Investigating the Use of {GPU}-Accelerated Nodes for {SAR} Image Formation },
booktitle = { Proc. of the IEEE International Conference on Cluster Computing, Workshop on Parallel Programming on Accelerator Clusters (PPAC) },
author = { Timothy D. R. Hartley and Ahmed R. Fasih and Charles A. Berdanier and F\"{u}sun {\"{O}}zg\"{u}ner and {\"U}mit V. \c{C}ataly\"{u}rek },
}
@poster { hartley09ipdps-poster,
year = { 2009 },
title = { High-Performance Filter-Stream Frameworks for Hierarchical, Heterogeneous, Distributed Supercomputers },
howpublished = { Poster, 23rd Int{\'}l. Parallel and Distributed Processing Symposium PhD Forum },
author = { Timothy D. R. Hartley and {\"U}mit V. \c{C}ataly\"{u}rek },
}
@article { Erdal09-JDI,
year = { 2009 },
volume = { 22 },
title = { A Knowledge-Anchored Integrative Image Search and Retrieval System },
pages = { 166-182 },
number = { 2 },
journal = { J. Digital Imaging },
author = { Selnur Erdal and {\"U}mit V. \c{C}ataly\"{u}rek and Philip R. O. Payne and Joel H. Saltz and Jyoti Kamal and Metin N. G\"{u}rcan },
}
@abstract { Devine09-DAGSTUHL,
year = { 2009 },
title = { Getting Started with Zoltan: A Short Tutorial },
series = { Dagstuhl Seminar Proceedings },
publisher = { Schloss Dagstuhl - Leibniz-Zentrum fuer Informatik },
number = { 09061 },
url = { http://drops.dagstuhl.de/opus/volltexte/2009/2088 },
editor = { Uwe Naumann and Olaf Schenk and Horst D. Simon and Sivan Toledo },
howpublished = { Abstract, Combinatorial Scientific Computing },
author = { Karen D. Devine and Erik G. Boman and Lee Ann Riesen and {\"U}mit V. \c{C}ataly\"{u}rek and Cedric Chevalier },
address = { Dagstuhl, Germany },
}
@inproceedings { Bozdag09-BICOB,
year = { 2009 },
volume = { 5462 },
title = { A Biclustering Method to Discover Co-regulated Genes Using Diverse Gene Expression Datasets },
series = { Lecture notes in Computer Science },
publisher = { Springer },
pages = { 151-163 },
doi = { 10.1007/978-3-642-00727-9_16 },
booktitle = { Proc. of 1st Int{\'}l. Conf. on Bioinformatics and Computational Biology },
author = { Doruk Bozda\u{g} and Jeffrey D. Parvin and {\"U}mit V. \c{C}ataly\"{u}rek },
}
@inproceedings { Bozdag09-CAMDA,
year = { 2009 },
title = { Parallel Computing Strategies for Sequence Mapping of NGS Data },
booktitle = { Extended abstract, 9th International Conference for the Critical Assesment of Massive Data Analysis },
author = { Doruk Bozda\u{g} and Terry Camerlengo and Hatice G. Ozer and Joanne Trgovcich and Tea Meulia and Kun Huang and {\"U}mit V. \c{C}ataly\"{u}rek },
}
@abstract { Bozdag09-Dagstuhl,
year = { 2009 },
title = { Parallelization of Mapping Algorithms for Next Generation Sequencing Applications },
series = { Dagstuhl Seminar Proceedings },
publisher = { Schloss Dagstuhl - Leibniz-Zentrum fuer Informatik },
number = { 09061 },
url = { http://drops.dagstuhl.de/opus/volltexte/2009/2129 },
howpublished = { Abstract, Combinatorial Scientific Computing },
author = { Doruk Bozda\u{g} and Catalin C. Barbacioru and {\"U}mit V. \c{C}ataly\"{u}rek },
address = { Dagstuhl, Germany },
}
@poster { Bozdag09-SC,
year = { 2009 },
title = { Combinatorial Algorithms Enabling Scientific Computing: Petascale Algorithms for Graph Coloring and Matching },
howpublished = { Poster, 21st Supercomputing Conference },
author = { Doruk Bozda\u{g} and {\"U}mit V. \c{C}ataly\"{u}rek and F. Dobrian and Assefaw H. Gebremedhin and Mahantesh Halappanavar and Alex Pothen },
}
@abstract { Bisseling09-DAGSTUHL,
year = { 2009 },
title = { Combinatorial Problems in High-Performance Computing: Partitioning },
series = { Dagstuhl Seminar Proceedings },
publisher = { Schloss Dagstuhl - Leibniz-Zentrum fuer Informatik },
number = { 09061 },
url = { http://drops.dagstuhl.de/opus/volltexte/2009/2081 },
editor = { Uwe Naumann and Olaf Schenk and Horst D. Simon and Sivan Toledo },
howpublished = { Abstract, Combinatorial Scientific Computing },
author = { Rob Bisseling and Tristan van Leeuwen and {\"U}mit V. \c{C}ataly\"{u}rek },
address = { Dagstuhl, Germany },
}
@incollection { Catalyurek09-IOS,
year = { 2009 },
volume = { 18 },
title = { Processing of Large-Scale Biomedical Images on a Cluster of Multi-Core {CPU}s and {GPU}s },
publisher = { IOS Press },
pages = { 341-364 },
url = { http://www.booksonline.iospress.nl/Content/View.aspx?piid=14174 },
editor = { W. Gentzsch and L. Grandinetti and G. Joubert },
booktitle = { High Performance and Large Scale Computing },
author = { {\"U}mit V. \c{C}ataly\"{u}rek and Timothy D. R. Hartley and Olcay Sertel and Manuel Ujaldon and Antonio Ruiz and Joel H. Saltz and Metin G\"{u}rcan },
}
@incollection { Catalyurek09-Wiley,
year = { 2009 },
title = { Hypergraph-based Dynamic Partitioning and Load Balancing },
publisher = { Wiley Publishing },
editor = { M. Parashar and X. Li and S. Chandra },
booktitle = { Advanced Computational Infrastructures for Parallel and Distributed Adaptive Applications },
author = { {\"U}mit V. \c{C}ataly\"{u}rek and Doruk Bozda\u{g} and Erik G. Boman and K.D. Devine and R. Heaphy and L.A. Fisk },
}
@phdthesis { Bozdag08-PhD,
year = { 2008 },
title = { Graph Coloring and Clustering Algorithms for Science and Engineering Applications },
month = { May },
key = { Bozdag08-PhD },
institution = { The Ohio State University, Biomedical Informatics },
author = { Doruk Bozda\u{g} },
}
@inproceedings { Khanna_SC08,
year = { 2008 },
title = { Using Overlays for Efficient Data Transfer over Shared Wide-Area Networks },
month = { Nov },
booktitle = { Proceedings of {SC2008} High Performance Computing, Networking, and Storage Conference },
author = { Gaurav Khanna and {\"U}mit V. \c{C}ataly\"{u}rek and Tahsin M. Kurc and Rajkumar Kettimuthu and P. Sadayappan and Ian Foster and Joel H. Saltz },
}
@article { Kumar08-TITB,
year = { 2008 },
volume = { 12 },
title = { Large-Scale Biomedical Image Analysis in Grid Environments },
pages = { 154-161 },
number = { 2 },
month = { Mar },
journal = { {IEEE} Transactions on Information Technology in Biomedicine },
doi = { 10.1109/TITB.2007.908466 },
author = { V.S. Kumar and B. Rutt and Tahsin M. Kurc and {\"U}mit V. \c{C}ataly\"{u}rek and Tony C. Pan and S. Chow and S. Lamont and M. Martone and Joel H. Saltz },
}
@inproceedings { Vydyanathan08-ICPP,
year = { 2008 },
title = { A Duplication Based Algorithm for Optimizing Latency Under Throughput Constraints for Streaming Workflows },
pages = { 254-261 },
doi = { 10.1109/ICPP.2008.68 },
booktitle = { 2008 International Conference on Parallel Processing (ICPP) },
author = { N. Vydyanathan and {\"U}mit V. \c{C}ataly\"{u}rek and Tahsin M. Kurc and P. Sadayappan and Joel H. Saltz },
}
@article { DeSupinski:2008,
year = { 2008 },
volume = { 22 },
title = { Bluegene/L applications: Parallelism on a massive scale },
pages = { 33--51 },
number = { 1 },
month = { Jan },
journal = { International Journal of High Performance Computing },
doi = { 10.1177/1094342007085025 },
author = { Bronis R de Supinski and Martin Schulz and Vasily V. Bulatov and William Cabot and Bor Chan and Andrew W Cook and Erik W Draegerl and James N Glosli and Jeffrey A Greenough and Keith Henderson and Alison Kubota and Steve Louis and Brian J Miller and Mehul V. Patel and Thomas E Spelce and Frederick H Streitz and Peter L Williams and Robert K Yates and Andy Yoo and George Almasi and Gyan Bhanot and Alan Gara and John A Gunnels and Manish Gupta and Jose Moreira and James Sexton and Bob Walkup and Charles Archer and Francois Gygi and Timothy C Germann and Kai Kadau and Peter S Lomdahl and Charles Rendleman and Michael L Welcome and William McLendon and Bruce Hendrickson and Franz Franchetti and Stefan Kraig and Juergen Lorenz and Christoph W Ueberhuber and Edmond Chow and {\"U}mit V. \c{C}ataly\"{u}rek },
}
@inproceedings { Khanna_IPDPS08,
year = { 2008 },
title = { A Dynamic Scheduling Approach for Coordinated Wide-Area Data Transfers using GridFTP },
booktitle = { Proc. of 22th International Parallel and Distributed Processing Symposium (IPDPS) },
author = { Gaurav Khanna and {\"U}mit V. \c{C}ataly\"{u}rek and Tahsin M. Kurc and Rajkumar Kettimuthu and P. Sadayappan and Joel H. Saltz },
address = { Miami, Florida },
}
@inproceedings { Hartley08,
year = { 2008 },
title = { Biomedical Image Analysis on a Cooperative Cluster of {GPU}s and Multicores },
pages = { 15-25 },
doi = { 10.1145/1375527.1375533 },
booktitle = { Proc. of the 22nd Annual International Conference on Supercomputing, ICS 2008 },
author = { Timothy D. R. Hartley and {\"U}mit V. \c{C}ataly\"{u}rek and Antonio Ruiz and F. Igual and R. Mayo and M. Ujaldon },
}
@article { Hakobyan08-NED,
year = { 2008 },
volume = { 238 },
title = { Dynamic generation of accident progression event trees },
pages = { 3457 - 3467 },
number = { 12 },
journal = { Nuclear Engineering and Design },
doi = { 10.1016/j.nucengdes.2008.08.005 },
author = { Aram Hakobyan and Tunc Aldemir and Richard Denning and Sean Dunagan and David Kunsman and Benjamin Rutt and {\"U}mit V. \c{C}ataly\"{u}rek },
}
@abstract { Bozdag08-CSC,
year = { 2008 },
title = { Parallel Distance-2 Coloring },
howpublished = { Abstract, Workshop on Combinatorial Scientific Computing and Petascale Simulations },
author = { Doruk Bozda\u{g} and {\"U}mit V. \c{C}ataly\"{u}rek and Assefaw H. Gebremedhin and F. Manne and Erik G. Boman },
}
@article { Bozdag08-JPDC,
year = { 2008 },
volume = { 68 },
title = { A framework for scalable greedy coloring on distributed-memory parallel computers },
pages = { 515--535 },
number = { 4 },
doi = { 10.1016/j.jpdc.2007.08.002 },
journal = { Journal of Parallel and Distributed Computing },
author = { Doruk Bozda\u{g} and Assefaw H. Gebremedhin and F. Manne and Erik G. Boman and {\"U}mit V. \c{C}ataly\"{u}rek },
}
@inproceedings { Boman08-JPCS,
year = { 2008 },
volume = { 125 },
title = { Combinatorial algorithms for computational science and engineering },
booktitle = { Journal of Physics: Conference Series },
author = { Erik G. Boman and Doruk Bozda\u{g} and {\"U}mit V. \c{C}ataly\"{u}rek and K. D. Devine and Assefaw H. Gebremedhin and P. D. Hovland and Alex Pothen },
}
@inproceedings { Catalyurek07-IPDPS,
year = { 2007 },
title = { Hypergraph-based Dynamic Load Balancing for Adaptive Scientific Computations },
pages = { 1-11 },
note = { Best Algorithms Paper Award },
month = { Mar },
booktitle = { Proc. of 21st Int{\'}l. Parallel and Distributed Processing Symposium },
author = { {\"U}mit V. \c{C}ataly\"{u}rek and Erik G. Boman and K.D. Devine and Doruk Bozda\u{g} and R. Heaphy and L.A. Fisk },
address = { Long Beach, CA },
}
@techreport { ZoltanUsersGuideV3,
note = { Tech. Report SAND2007-4748W \url{http://www.cs.sandia.gov/Zoltan/ug_html/ug.html} },
year = { 2007 },
address = { Albuquerque, NM },
institution = { Sandia National Laboratories },
author = { Erik Boman and Karen Devine and Lee Ann Fisk and Robert Heaphy and Bruce Hendrickson and Courtenay Vaughan and {\"U}mit V. \c{C}ataly\"{u}rek and Doruk Bozda\u{g} and William Mitchell and James Teresco },
title = { {Zoltan 3.0}: Parallel Partitioning, Load-balancing, and Data Management Services; User\'s Guide },
}
@techreport { ZoltanDevelopersGuideV3,
note = { Tech. Report SAND2007-4749W, \url{http://www.cs.sandia.gov/Zoltan/dev_html/dev.html} },
year = { 2007 },
address = { Albuquerque, NM },
institution = { Sandia National Laboratories },
author = { Erik Boman and Karen Devine and Lee Ann Fisk and Robert Heaphy and Bruce Hendrickson and Courtenay Vaughan and {\"U}mit V. \c{C}ataly\"{u}rek and Doruk Bozda\u{g} and William Mitchell and James Teresco },
title = { {Zoltan 3.0}: Parallel Partitioning, Load-balancing, and Data Management Services; Developer\'s Guide },
}
@inproceedings { Weng07-Grid,
year = { 2007 },
title = { Optimizing multiple queries on scientific datasets with partial replicas },
pages = { 259-266 },
doi = { 10.1109/GRID.2007.4354141 },
booktitle = { Proc. of 8th IEEE/ACM International Conference on Grid Computing (GRID 2007) },
author = { L. Weng and {\"U}mit V. \c{C}ataly\"{u}rek and Tahsin M. Kurc and G. Agrawal and Joel H. Saltz },
}
@inproceedings { Vydyanathan07,
year = { 2007 },
title = { Toward Optimizing Latency Under Throughput Constraints for Application Workflows on Clusters },
pages = { 173-183 },
doi = { 10.1007/978-3-540-74466-5_20 },
booktitle = { Proceedings of the 13th International Euro-Par Conference (Euro-Par 2007) },
author = { Nagavijayalakshmi Vydyanathan and {\"U}mit V. \c{C}ataly\"{u}rek and Tahsin M. Kurc and P. Sadayappan and Joel H. Saltz },
}
@inproceedings { Tavares07-CCGRID,
year = { 2007 },
title = { An Efficient and Reliable Scientific Workflow System },
pages = { 445-452 },
doi = { 10.1109/CCGRID.2007.20 },
booktitle = { Prof. of Seventh IEEE International Symposium on Cluster Computing and the Grid (CCGrid 2007) },
author = { T. Tavares and G. Teodoro and Tahsin M. Kurc and R. Ferreira and D. Neto and W. Meira and {\"U}mit V. \c{C}ataly\"{u}rek and S. Hastings and S. Oster and S. Langella and Joel H. Saltz },
}
@inproceedings { ruiz07,
year = { 2007 },
title = { Pathological image analysis using the {GPU}: Stroma classification for neuroblastoma },
pages = { 78--85 },
booktitle = { Proc. of IEEE Int. Conf. on Bioinformatics and Biomedicine },
author = { Antonio Ruiz and Olcay Sertel and Manuel Ujaldon and {\"U}mit V. \c{C}ataly\"{u}rek and Joel H. Saltz and M. G\"{u}rcan },
}
@inproceedings { Kumar07-CLUSTER,
year = { 2007 },
title = { Performance vs. accuracy trade-offs for large-scale image analysis applications },
pages = { 100-109 },
doi = { 10.1109/CLUSTR.2007.4629222 },
booktitle = { Proc. of the 2007 IEEE International Conference on Cluster Computing },
author = { V. S. Kumar and Tahsin M. Kurc and Jun Kong and {\"U}mit V. \c{C}ataly\"{u}rek and M. N. G\"{u}rcan and Joel H. Saltz },
}
@inproceedings { Khanna07,
year = { 2007 },
title = { Scheduling File Transfers for Data-Intensive Jobs on Heterogeneous Clusters },
pages = { 214-223 },
doi = { 10.1007/978-3-540-74466-5_24 },
booktitle = { Proceedings of the 13th International Euro-Par Conference (Euro-Par 2007) },
author = { G. Khanna and {\"U}mit V. \c{C}ataly\"{u}rek and Tahsin M. Kurc and P. Sadayappan and Joel H. Saltz },
}
@poster { hartley07sc,
year = { 2007 },
title = { Storing and Searching Massive Scale-free Graphs },
howpublished = { Poster, 19th Supercomputing Conference, 2nd Place Student Poster },
author = { Timothy D. R. Hartley and {\"U}mit V. \c{C}ataly\"{u}rek and Andy Yoo },
}
@inproceedings { Gurcan2007-AMIA,
year = { 2007 },
title = { Computerized pathological image analysis for neuroblastoma prognosis },
booktitle = { 2007 AMIA Annual Symposium },
author = { Metin N. G\"{u}rcan and Jun Kong. and Olcay Sertel and Barla B. Cambazoglu and Joel H. Saltz and {\"U}mit V. \c{C}ataly\"{u}rek },
}
@inproceedings { Cambazoglu07,
year = { 2007 },
title = { Efficient Processing of Pathological Images Using the Grid: Computer-Aided Prognosis of Neuroblastoma },
booktitle = { Proceedings of the International Workshop on Challenges of Large Applications in Distributed Environments (CLADE 07) },
author = { Barla B. Cambazoglu and Olcay Sertel and Jun Kong and Joel H. Saltz and Metin N. G\"{u}rcan and {\"U}mit V. \c{C}ataly\"{u}rek },
}
@inproceedings { Boman07-JPCS,
year = { 2007 },
volume = { 78 },
title = { Enabling high performance computational science through combinatorial algorithms },
pages = { 012058 (10pp) },
booktitle = { Journal of Physics: Conference Series },
author = { Erik G. Boman and Doruk Bozda\u{g} and {\"U}mit V. \c{C}ataly\"{u}rek and K. D. Devine and Assefaw H. Gebremedhin and P. D. Hovland and Alex Pothen and M. M. Strout },
}
@inproceedings { Vydyanathan06c,
year = { 2006 },
title = { Locality Conscious Processor Allocation and Scheduling for Mixed Parallel Applications },
organization = { IEEE Computer Society },
month = { Sep },
booktitle = { Proceedings of 2006 IEEE International Conference on Cluster Computing },
author = { Nagavijayalakshmi Vydyanathan and Sriram Krishnamoorthy and Gerald Sabin and {\"U}mit V. \c{C}ataly\"{u}rek and Tahsin M. Kurc and P. Sadayappan and Joel H. Saltz },
}
@inproceedings { DUcar06,
year = { 2006 },
title = { Improving Functional Modularity in Protein-Protein Interactions Graphs Using Hub-induced Subgraphs },
month = { Sep },
booktitle = { In Proceedings of the European Conference on Principles and Practice of Knowledge Discovery in Databases (PKDD) },
author = { D. Ucar and S. Asur and {\"U}mit V. \c{C}ataly\"{u}rek and S. Parthasarathy },
address = { Berlin, Germany },
}
@inproceedings { Hartley06,
year = { 2006 },
title = { {MSSG}: A Framework for Massive Scale Semantic Graphs },
organization = { IEEE Computer Society },
month = { Sep },
booktitle = { Proceedings of 2006 IEEE International Conference on Cluster Computing },
author = { Timothy D. R. Hartley and {\"U}mit V. \c{C}ataly\"{u}rek and F\"{u}sun {\"{O}}zg\"{u}ner and Andy Yoo and Scott Kohn and Keith Henderson },
}
@inproceedings { Weng06,
year = { 2006 },
title = { Using Space and Attribute Partitioned Partial Replicas for Data Subsetting and Aggregation Queries },
month = { Aug },
booktitle = { 2006 International Conference on Parallel Processing },
author = { Li Weng and {\"U}mit V. \c{C}ataly\"{u}rek and Tahsin M. Kurc and Gagan Agrawal and Joel H. Saltz },
}
@inproceedings { Narayanan06,
year = { 2006 },
title = { On Creating Efficient Object-relational Views of Scientific Datasets },
month = { Aug },
booktitle = { 2006 International Conference on Parallel Processing },
author = { Sivaramakrishnan Narayanan and Tahsin M. Kurc and {\"U}mit V. \c{C}ataly\"{u}rek and Joel H. Saltz },
}
@inproceedings { Khanna06,
year = { 2006 },
title = { Task Scheduling and File Replication for Data-Intensive Jobs with Batch-shared {I/O} },
pages = { 241-252 },
month = { Jun },
booktitle = { Proceedings of the Fifteen International Symposium on High Performance Distributed Computing (HPDC-15) },
author = { Gaurav Khanna and Nagavijayalakshmi Vydyanathan and {\"U}mit V. \c{C}ataly\"{u}rek and Tahsin M. Kurc and Sriram Krishnamoorthy and P. Sadayappan and Joel H. Saltz },
address = { Paris, France },
}
@inproceedings { Khanna06b,
year = { 2006 },
title = { A Data Locality Aware Online Scheduling Approach for I/O-Intensive Jobs with File Sharing },
month = { Jun },
booktitle = { Proceedings of the 12th International Workshop on Job Scheduling Strategies for Parallel Processing (JSSPP 2006), In Conjunction with SIGMETRICS 2006 },
author = { Gaurav Khanna and {\"U}mit V. \c{C}ataly\"{u}rek and Tahsin M. Kurc and P. Sadayappan and Joel H. Saltz },
address = { Saint-Malo, France },
}
@inproceedings { Bozdag06-HCW,
year = { 2006 },
title = { A task duplication based bottom-up scheduling algorithm for heterogeneous environments },
month = { Apr },
doi = { 10.1109/IPDPS.2006.1639389 },
booktitle = { 15th International Heterogeneous Computing Workshop (in conjunction with IPDPS) },
author = { Doruk Bozda\u{g} and {\"U}mit V. \c{C}ataly\"{u}rek and F. {\"{O}}zg\"{u}ner },
address = { Rhodes Island, Greece },
}
@article { Zhang06-IJHPCA,
year = { 2006 },
volume = { 20 },
title = { Supporting Scalable and Distributed Data Subsetting and Aggregation in Large-scale Seismic Data Analysis },
pages = { 423--438 },
number = { 3 },
journal = { The Journal of High Performance Computing Applications },
author = { Xi Zhang and Benjamin Rutt and {\"U}mit V. \c{C}ataly\"{u}rek and Tahsin M. Kurc and Joel H. Saltz },
}
@inproceedings { Vydyanathan06-HCW,
year = { 2006 },
title = { Scheduling of Tasks with Batch-shared I/O on Heterogeneous Systems },
booktitle = { Proceedings of 20th International Parallel and Distributed Processing Symposium (IPDPS), Heterogeneous Computing Workshop (HCW 2006) },
author = { Nagavijayalakshmi Vydyanathan and Gaurav Khanna and Tahsin M. Kurc and {\"U}mit V. \c{C}ataly\"{u}rek and Pete Wyckoff and Joel H. Saltz and P. Sadayappan },
}
@inproceedings { Vydyanathan06b,
year = { 2006 },
booktitle = { 2006 International Conference on Parallel Processing },
title = { An Integrated Approach for Processor Allocation and Scheduling of Mixed-Parallel Applications },
author = { Nagavijayalakshmi Vydyanathan and Sriram Krishnamoorthy and Gerald Sabin and {\"U}mit V. \c{C}ataly\"{u}rek and Tahsin M. Kurc and P. Sadayappan and Joel H. Saltz },
}
@inproceedings { Kumar06-SC,
year = { 2006 },
booktitle = { Proceedings of {SC2006} High Performance Computing, Networking, and Storage Conference },
title = { Large Image Correction and Warping in a Cluster Environment },
author = { Vijay S. Kumar and Benjamin Rutt and Tahsin M. Kurc and {\"U}mit V. \c{C}ataly\"{u}rek and Sunny Chow and Stephan Lamont and Maryann Martone and Joel H. Saltz },
}
@inproceedings { krishnamoorthy06-POHLL,
year = { 2006 },
address = { Rhodes Island, Greece },
booktitle = { Proceedings of 20th International Parallel and Distributed Processing Symposium (IPDPS), Workshop on Performance Optimization for High-Level Languages and Libraries (POHLL 2006) },
title = { An Approach to Locality-Conscious Load Balancing and Transparent Memory Hierarchy Management with a Global-Address-Space Parallel Programming Model },
author = { Sriram Krishnamoorthy and {\"U}mit V. \c{C}ataly\"{u}rek and Jarek Nieplocha and P. Sadayappan },
}
@inproceedings { Krishnamoorthy06-SC,
year = { 2006 },
booktitle = { Proceedings of {SC2006} High Performance Computing, Networking, and Storage Conference },
title = { Hypergraph Partitioning for Automatic Memory Hierarchy Management },
author = { Sriram Krishnamoorthy and {\"U}mit V. \c{C}ataly\"{u}rek and Jarek Nieplocha and Atanas Rountev and P. Sadayappan },
}
@inproceedings { krishnamoorthy2006-NGS,
year = { 2006 },
address = { Rhodes Island, Greece },
booktitle = { Proc. {IPDPS} Workshop on {N}ext {G}eneration {S}oftware },
title = { An Extensible Global Address Space Framework with Decoupled Task and Data Abstractions },
author = { Sriram Krishnamoorthy and {\"U}mit V. \c{C}ataly\"{u}rek and Jarek Nieplocha and Atanas Rountev and P. Sadayappan },
}
@inproceedings { Devine06,
year = { 2006 },
doi = { 10.1109/IPDPS.2006.1639359 },
publisher = { IEEE },
booktitle = { Proceedings of 20th International Parallel and Distributed Processing Symposium (IPDPS) },
title = { Parallel Hypergraph Partitioning for Scientific Computing },
author = { K.D. Devine and Erik G. Boman and R.T. Heaphy and R.H. Bisseling and {\"U}mit V. \c{C}ataly\"{u}rek },
}
@inproceedings { Rutt05,
year = { 2005 },
address = { Boston, MA },
month = { Sep },
booktitle = { The 2005 IEEE International Conference on Cluster Computing },
title = { Distributed Out-of-Core Preprocessing of Very Large Microscopy Images for Efficient Querying },
author = { Benjamin Rutt and Vijay S. Kumar and Tony C. Pan and Tahsin M. Kurc and {\"U}mit V. \c{C}ataly\"{u}rek and Yujun Wang and Joel H. Saltz },
}
@inproceedings { Narayanan05B,
year = { 2005 },
pages = { 98--109 },
month = { Sep },
booktitle = { Proceedings of {VLDB} Workshop Data Management in Grid 2005 ({VLDB DMG\'05} },
title = { Servicing Seismic and Oil Reservoir Simulation Data through Grid Data Services },
author = { Sivaramakrishnan Narayanan and Tahsin M. Kurc and {\"U}mit V. \c{C}ataly\"{u}rek and Joel H. Saltz },
}
@article { Kurc05,
year = { 2005 },
volume = { 17 },
title = { A Simulation and Data Analysis System for Large Scale,Data-Driven Oil Reservoir Simulation Studies },
pages = { 1441--1467 },
number = { 11 },
month = { Sep },
journal = { Concurrency and Computation: Practice and Experience. },
author = { Tahsin M. Kurc and {\"U}mit V. \c{C}ataly\"{u}rek and X. Zhang and Joel H. Saltz and R. Martino and Mary F. Wheeler and M. Peszynska and Alan Sussman and C. Hansen and M. Sen and R. Seifoullaev and P. Stoffa and C. Torres-Verdin and Manish Parashar },
}
@inproceedings { Bozdag05-HPCC,
year = { 2005 },
volume = { 3726 },
title = { A Parallel Distance-2 Graph Coloring Algorithm for Distributed Memory Computers },
series = { Lecture notes in Computer Science },
publisher = { Springer },
pages = { 796--806 },
month = { Sep },
doi = { 10.1007/11557654_90 },
booktitle = { Proc. of 1st Int{\'}l. Conf. on High Performance Computing and Communications },
author = { Doruk Bozda\u{g} and {\"U}mit V. \c{C}ataly\"{u}rek and Assefaw H. Gebremedhin and F. Manne and Erik G. Boman and F. {\"{O}}zg\"{u}ner },
address = { Sorrento, Italy },
}
@inproceedings { Boman05-EuroPar,
year = { 2005 },
volume = { 3648 },
title = { A Scalable Parallel Graph Coloring Algorithm for Distributed Memory Computers },
series = { Lecture notes in Computer Science },
publisher = { Springer },
pages = { 241--251 },
month = { Aug },
doi = { 10.1007/11549468_29 },
booktitle = { Proc. of 11th Int{\'}l. Euro-Par Conf. on Parallel Processing },
author = { Erik G. Boman and Doruk Bozda\u{g} and {\"U}mit V. \c{C}ataly\"{u}rek and Assefaw H. Gebremedhin and F. Manne },
address = { Lisbon, Portugal },
}
@inproceedings { Bozdag05-ICPP,
year = { 2005 },
title = { A Task Duplication Based Scheduling Algorithm Using Partial Schedules },
pages = { 630--637 },
month = { Jun },
doi = { 10.1109/ICPP.2005.15 },
booktitle = { Proc. of 34th Int{\'}l. Conf. on Parallel Processing },
author = { Doruk Bozda\u{g} and F. {\"{O}}zg\"{u}ner and E. Ekici and {\"U}mit V. \c{C}ataly\"{u}rek },
address = { Oslo, Norway },
}
@inproceedings { Weng05,
year = { 2005 },
title = { Servicing Range Queries on Multidimensional Datasets with Partial Replicas },
month = { May },
booktitle = { Proceedings of the 5th IEEE/ACM International Symposium on Cluster Computing and the Grid (CCGrid 2005) },
author = { Li Weng and {\"U}mit V. \c{C}ataly\"{u}rek and Tahsin M. Kurc and Gagan Agrawal and Joel H. Saltz },
}
@inproceedings { Khanna05,
doi = { 10.1109/CCGRID.2005.1558643 },
year = { 2005 },
title = { A Hypergraph Partitioning Based Approach for Scheduling of Tasks with Batch-shared {I/O} },
month = { May },
booktitle = { Proceedings of the 5th IEEE/ACM International Symposium on Cluster Computing and the Grid (CCGrid 2005) },
author = { Gaurav Khanna and Nagavijayalakshmi Vydyanathan and Tahsin M. Kurc and {\"U}mit V. \c{C}ataly\"{u}rek and Pete Wyckoff and Joel H. Saltz and P. Sadayappan },
}
@techreport { ZoltanParHypPar05tr,
year = { 2005 },
title = { Parallel Hypergraph Partitioning for Scientific Computing },
number = { SAND2005-2796C },
month = { Apr },
institution = { Sandia National Laboratories },
author = { Erik G. Boman and K.D. Devine and R.T. Heaphy and {\"U}mit V. \c{C}ataly\"{u}rek and R.H. Bisseling },
address = { Albuquerque, NM },
}
@inproceedings { Narayanan05,
year = { 2005 },
title = { A Runtime Framework for Partial Replication and Its Application for On-Demand Data Exploration },
month = { Mar },
booktitle = { High Performance Computing Symposium (HPC 2005), SCS Spring Simulation Multiconference },
author = { Sivaramakrishnan Narayanan and {\"U}mit V. \c{C}ataly\"{u}rek and Tahsin M. Kurc and Vijay S. Kumar and Joel H. Saltz },
}
@inproceedings { Kumar05,
year = { 2005 },
title = { Design and Implementation of a Data Server Using a Peer-to-Peer Storage System },
month = { Mar },
booktitle = { High Performance Computing Symposium (HPC 2005), SCS Spring Simulation Multiconference },
author = { Vijay S. Kumar and Tahsin M. Kurc and {\"U}mit V. \c{C}ataly\"{u}rek and Joel H. Saltz },
}
@inproceedings { Yoo05,
year = { 2005 },
doi = { 10.1109/SC.2005.4 },
title = { A Scalable Distributed Parallel Breadth-First Search Algorithm on {BlueGene/L} },
note = { Gordon Bell Finalist. },
booktitle = { Proceedings of {SC2005} High Performance Computing, Networking, and Storage Conference },
author = { Andy Yoo and Edmond Chow and Keith Henderson and William McLendon and Bruce Hendrickson and {\"U}mit V. \c{C}ataly\"{u}rek },
}
@incollection { Ribeiro05,
year = { 2005 },
title = { Tools for Efficient Subsetting and Pipelined Processing of Large Scale, Distributed Biomedical Image Data },
publisher = { Elsevier },
editor = { Lucio Grandinetti },
booktitle = { Grid Computing: The New Frontier Of High Performance Computing, 14 },
author = { M. Ribeiro and Tahsin M. Kurc and Tony C. Pan and K. Huang and {\"U}mit V. \c{C}ataly\"{u}rek and X. Zhang and S. Langella and S. Hastings and S. Oster and R. Ferreira and Joel H. Saltz },
}
@inproceedings { DBLP:conf/iccS/ParasharMBKRKCSW05,
year = { 2005 },
title = { Towards Dynamic Data-Driven Optimization of Oil Well Placement. },
pages = { 656-663 },
doi = { 10.1007/11428848_85 },
booktitle = { International Conference on Computational Science (2) },
author = { Manish Parashar and Vincent Matossian and Wolfgang Bangerth and Hector Klie and Benjamin Rutt and Tahsin M. Kurc and {\"U}mit V. \c{C}ataly\"{u}rek and Joel H. Saltz and Mary F. Wheeler },
}
@article { Parashar2005-FGCS,
year = { 2005 },
volume = { 21 },
title = { Application of Grid-enabled technologies for solving optimization problems in data-driven reservoir studies },
pages = { 19--26 },
number = { 1 },
month = { Jan },
journal = { Future Generation Computer Systems },
doi = { 10.1016/j.future.2004.09.028 },
author = { Manish Parashar and Hector Klie and {\"U}mit V. \c{C}ataly\"{u}rek and Tahsin M. Kurc and Vincent Matossian and Joel H. Saltz and Mary F. Wheeler },
}
@article { Hastings05,
year = { 2005 },
volume = { 34 },
title = { XML database support for distributed execution of data-intensive scientific workflows. },
pages = { 50-55 },
number = { 3 },
doi = { 10.1145/1084805.1084815 },
journal = { SIGMOD Record },
author = { Shannon Hastings and Matheus Ribeiro and Stephen Langella and Scott Oster and {\"U}mit V. \c{C}ataly\"{u}rek and Tony C. Pan and Kun Huang and Renato Ferreira and Joel H. Saltz and Tahsin M. Kurc },
}
@inproceedings { Langella04,
year = { 2004 },
title = { A Distributed Data Management Middleware for Data-Driven Application Systems },
month = { Sep },
booktitle = { Proceedings of 2004 IEEE International Conference on Cluster Computing },
author = { Stephen Langella and Shannon Hastings and Scott Oster and Tahsin M. Kurc and {\"U}mit V. \c{C}ataly\"{u}rek and Joel H. Saltz },
}
@inproceedings { Zhang04B,
year = { 2004 },
doi = { 10.1109/HPDC.2004.1323471 },
address = { Honolulu, HI },
publisher = { IEEE Press },
month = { Jun },
booktitle = { Proceedings of the Thirteen International Symposium on High Performance Distributed Computing (HPDC-13) },
author = { Xi Zhang and Tahsin M. Kurc and Tony C. Pan and {\"U}mit V. \c{C}ataly\"{u}rek and Sivaramakrishnan Narayanan and Pete Wyckoff and Joel H. Saltz },
title = { Strategies for Using Additional Resources in Parallel Hash-based Join Algorithms },
}
@inproceedings { Weng04,
year = { 2004 },
doi = { 10.1109/HPDC.2004.1323476 },
address = { Honolulu, HI },
publisher = { IEEE Press },
month = { Jun },
booktitle = { Proceedings of the Thirteen International Symposium on High Performance Distributed Computing (HPDC-13) },
author = { Li Weng and Gagan Agrawal and {\"U}mit V. \c{C}ataly\"{u}rek and Tahsin M. Kurc and Sivaramakrishnan Narayanan and Joel H. Saltz },
title = { An Approach for Automatic Data Virtualization },
}
@inproceedings { Parashar04,
year = { 2004 },
pages = { 805-812 },
month = { Jun },
booktitle = { Proceedings of Workshop on Dynamic Data Driven Application Systems (International Conference on Computational Science) },
author = { Manish Parashar and H. Klie and {\"U}mit V. \c{C}ataly\"{u}rek and Tahsin M. Kurc and V. Matossian and Joel H. Saltz and Mary F. Wheeler },
title = { Application of Grid-enabled Technologies for Solving Optimization Problems in Data-Driven Reservoir Studies },
}
@inproceedings { Zhang04,
doi = { 10.1109/CCGrid.2004.1336605 },
year = { 2004 },
title = { Serving Queries to Multi-Resolution Datasets on Disk-based Storage Clusters },
month = { Apr },
booktitle = { Proceedings of 4th IEEE/ACM International Symposium on Cluster Computing and the Grid (CCGrid2004) },
author = { Xi Zhang and Tony C. Pan and {\"U}mit V. \c{C}ataly\"{u}rek and Tahsin M. Kurc and Joel H. Saltz },
address = { Chicago, IL },
}
@inproceedings { Weng04B,
doi = { 10.1007/11532378_21 },
year = { 2004 },
title = { Supporting SQL-3 Aggregations on Grid-based Data Repositories },
booktitle = { Proceedings of the 17th International Workshop on Languages and Compilers for Parallel Computing },
author = { Li Weng and Gagan Agrawal and {\"U}mit V. \c{C}ataly\"{u}rek and Joel H. Saltz },
}
@inproceedings { Vydyanathan04,
doi = { 10.1109/GRID.2004.63 },
year = { 2004 },
title = { Use of PVFS for Efficient Execution of Jobs with Pipeline-Shared I/O },
booktitle = { Proceedings of the 5th IEEE/ACM International Workshop on Grid Computing (Grid 2004) },
author = { Nagavijayalakshmi Vydyanathan and Gaurav Khanna and Tahsin M. Kurc and {\"U}mit V. \c{C}ataly\"{u}rek and Pete Wyckoff and Joel H. Saltz and P. Sadayappan },
}
@article { Aykanat04,
doi = { 10.1137/S1064827502401953 },
year = { 2004 },
volume = { 26 },
title = { Permuting Sparse Rectangular Matrices into Block-Diagonal Form },
pages = { 1860--1879 },
number = { 6 },
journal = { {SIAM} Journal on Scientific Computing (SISC) },
author = { Cevdet Aykanat and Ali P{\i}nar and {\"U}mit V. \c{C}ataly\"{u}rek },
}
@article { Catalyurek03B,
doi = { 10.1109/TITB.2004.823952 },
year = { 2003 },
volume = { 7 },
title = { The Virtual Microscope },
pages = { 230--248 },
number = { 4 },
month = { Dec },
journal = { {IEEE} Transactions on Information Technology in BioMedicine },
author = { {\"U}mit V. \c{C}ataly\"{u}rek and Michael D. Beynon and Chialin Chang and Tahsin M. Kurc and Alan Sussman and Joel H. Saltz },
}
@inproceedings { Narayanan03B,
year = { 2003 },
doi = { 10.1109/GRID.2003.1261709 },
address = { Phoenix, Arizona },
pages = { 141--148 },
month = { Nov },
booktitle = { Proceedings of the Fourth International Workshop on Grid Computing (Grid 2003) },
author = { Sivaramakrishnan Narayanan and {\"U}mit V. \c{C}ataly\"{u}rek and Tahsin M. Kurc and Xi Zhang and Joel H. Saltz },
title = { Applying Database Support for Large Scale Data Driven Science in Distributed Environments },
}
@inproceedings { Kurc03B,
year = { 2003 },
doi = { 10.1145/1048935.1050160 },
address = { Phoenix, {AZ} },
month = { Nov },
booktitle = { ACM/IEEE {SC2003} },
author = { Tahsin M. Kurc and Feng Lee and Gagan Agrawal and {\"U}mit V. \c{C}ataly\"{u}rek and Renato Ferreira and Joel H. Saltz },
title = { Optimizing Reduction Computations In a Distributed Environment },
}
@inproceedings { SALTZ03,
year = { 2003 },
address = { Melbourne, Australia },
month = { Jun },
booktitle = { Dynamic Data Driven Application Systems Workshop, held jointly with ICCS 2003 },
author = { Joel H. Saltz and {\"U}mit V. \c{C}ataly\"{u}rek and Tahsin M. Kurc and M. Gray and S. Hastings and S. Langella and S. Narayanan and R. Martino and S. Bryant and M. Peszynska and Mary F. Wheeler and Alan Sussman and Michael D. Beynon and C. Hansen and D. Stredney and D. Sessanna },
title = { Driving Scientific Applications by Data in Distributed Environments },
}
@inproceedings { Balaji03,
year = { 2003 },
doi = { 10.1109/HPDC.2003.1210013 },
publisher = { IEEE Press },
month = { Jun },
booktitle = { Proceedings of the Twelfth International Symposium on High Performance Distributed Computing (HPDC-12) },
author = { Pavan Balaji and Jiesheng Wu and Tahsin M. Kurc and {\"U}mit V. \c{C}ataly\"{u}rek and Dhabaleswar K. Panda and Joel H. Saltz },
title = { Impact of High Performance Sockets on Data Intensive Applications },
}
@inproceedings { Hastings03,
year = { 2003 },
title = { Image Processing for the Grid: A Toolkit for Building Grid-enabled Image Processing Applications. },
publisher = { IEEE Press },
month = { May },
booktitle = { CCGrid: IEEE International Symposium on Cluster Computing and the Grid },
author = { Shannon Hastings and Tahsin M. Kurc and Steve Langella and {\"U}mit V. \c{C}ataly\"{u}rek and Tony C. Pan and Joel H. Saltz },
}
@inproceedings { Catalyurek03,
year = { 2003 },
title = { A Component-based Implementation of Multiple Sequence Alignment },
month = { Mar },
booktitle = { 18th ACM Symposium on Applied Computing (SAC2003) Bioinformatics Track },
author = { {\"U}mit V. \c{C}ataly\"{u}rek and Mike Gray and Tahsin M. Kurc and Joel H. Saltz and Eric Stahlberg and Renato Ferreira },
address = { Melbourne, FL },
}
@article { Narayanan03,
doi = { 10.1142/S0129626403001264 },
year = { 2003 },
volume = { 13 },
title = { Database Support for Data-driven Scientific Applications in the Grid },
pages = { 245--271 },
number = { 2 },
journal = { Parallel Processing Letters },
author = { Sivaramakrishnan Narayanan and Tahsin M. Kurc and {\"U}mit V. \c{C}ataly\"{u}rek and Joel H. Saltz },
}
@inproceedings { Kurc03,
year = { 2003 },
title = { A Distributed Execution Environment for Analysis of {DCE-MR} Image Datasets },
booktitle = { The Society for Computer Applications in Radiology (SCAR 2003) },
author = { Tahsin M. Kurc and S. Hastings and {\"U}mit V. \c{C}ataly\"{u}rek and Joel H. Saltz and J. D. Fleig and B. D. Clymer and H. von Tengg-Kobligk and K. T. Baudendistel and R. Machiraju and M. V. Knopp },
}
@inproceedings { Spencer02,
year = { 2002 },
title = { Executing Multiple Pipelined Data Analysis Operations in the {Grid} },
publisher = { ACM Press },
month = { Nov },
booktitle = { Proceedings of the 2002 ACM/IEEE SC02 Conference },
author = { Matthew Spencer and Renato Ferreira and Michael Beynon and Tahsin M. Kurc and {\"U}mit V. \c{C}ataly\"{u}rek and Alan Sussman and Joel H. Saltz },
}
@techreport { Catalyurek02C,
year = { 2002 },
title = { The Virtual Microscope },
number = { CS-TR-xxxx and UMIACS-TR-2002-xx },
month = { Oct },
institution = { University of Maryland, Department of Computer Science and UMIACS },
author = { {\"U}mit V. \c{C}ataly\"{u}rek and Michael D. Beynon and Chialin Chang and Tahsin M. Kurc and Alan Sussman and Joel H. Saltz },
annote = { VM-TechRep },
}
@article { BEYNON02B,
year = { 2002 },
volume = { 28 },
title = { Processing Large-Scale Multidimensional Data in Parallel and Distributed Environments },
pages = { 827--859 },
number = { 5 },
note = { Special Issue on Data Intensive Computing },
month = { May },
journal = { Parallel Computing },
author = { Michael Beynon and Chialin Chang and {\"U}mit V. \c{C}ataly\"{u}rek and Tahsin M. Kurc and Alan Sussman and Henrique Andrade and Renato Ferreira and Joel H. Saltz },
}
@inproceedings { Beynon02C,
year = { 2002 },
title = { Efficient Manipulation of Large Datasets on Heterogeneous Storage Systems },
month = { Apr },
booktitle = { Proceedings of 16th International Parallel and Distributed Processing Symposium ({IPDPS}) },
author = { Michael D. Beynon and Tahsin M. Kurc and {\"U}mit V. \c{C}ataly\"{u}rek and Alan Sussman and Joel H. Saltz },
address = { Fort Lauderdale, Florida },
}
@inproceedings { Catalyurek02B,
year = { 2002 },
title = { Improving Performance of Multiple Sequence Alignment Analysis in Multi-client Environments },
month = { Apr },
booktitle = { Proceedings of 16th International Parallel and Distributed Processing Symposium ({IPDPS}), First Workshop on High Performance Computational Biology },
author = { {\"U}mit V. \c{C}ataly\"{u}rek and Eric Stahlberg and Renato Ferreira and Tahsin M. Kurc and Joel H. Saltz },
address = { Fort Lauderdale, Florida },
}
@inproceedings { ANDRADE02D,
year = { 2002 },
title = { Persistent Caching in a Multiple Query Optimization Framework },
publisher = { Springer-Verlag },
month = { Mar },
booktitle = { Proceedings of the Sixth Workshop on Languages, Compilers and Run-time Systems for Scalable Computers },
author = { Henrique Andrade and Tahsin M. Kurc and {\"U}mit V. \c{C}ataly\"{u}rek and Alan Sussman and Joel H. Saltz },
}
@inproceedings { Catalyurek01-SC,
pdf = { Catalyurek01-SC.pdf },
doi = { 10.1109/SC.2001.10035 },
year = { 2001 },
title = { A Hypergraph-Partitioning Approach for Coarse-Grain Decomposition },
month = { Nov },
key = { CATALYUREK01C },
booktitle = { ACM/IEEE {SC2001} },
author = { {\"U}mit V. \c{C}ataly\"{u}rek and Cevdet Aykanat },
address = { Denver, {CO} },
}
@article { Beynon01-ParCo,
year = { 2001 },
doi = { 10.1016/S0167-8191(01)00099-0 },
volume = { 27 },
title = { Distributed Processing of Very Large Datasets with {DataCutter} },
pages = { 1457--1478 },
number = { 11 },
month = { Oct },
url = { http://linkinghub.elsevier.com/retrieve/pii/S0167819101000990 },
journal = { Parallel Computing },
author = { Michael D. Beynon and Tahsin M. Kurc and {\"U}mit V. \c{C}ataly\"{u}rek and Chialin Chang and Alan Sussman and Joel H. Saltz },
}
@inproceedings { BEYNON01D,
year = { 2001 },
month = { Aug },
booktitle = { Proceedings of the Third Annual International Workshop on Active Middleware Services (AMS2001) },
author = { Michael D. Beynon and Alan Sussman and {\"U}mit V. \c{C}ataly\"{u}rek and Tahsin M. Kurc and Joel H. Saltz },
annote = { DataCutter },
title = { Performance Optimization for Data Intensive Grid Applications },
}
@article { Catalyurek01A,
year = { 2001 },
volume = { 125 },
number = { 8 },
month = { Aug },
key = { CATALYUREK01A },
journal = { Archives of Pathology and Laboratory Medicine },
author = { {\"U}mit V. \c{C}ataly\"{u}rek and Tahsin M. Kurc and Alan Sussman and Joel H. Saltz },
title = { Improving the Performance and Functionality of the Virtual Microscope },
}
@article { Kurc01B,
year = { 2001 },
volume = { 21 },
pages = { 24--33 },
number = { 4 },
month = { Jul/Aug },
journal = { IEEE Computer Graphics and Applications },
author = { Tahsin M. Kurc and {\"U}mit V. \c{C}ataly\"{u}rek and Chialin Chang and Alan Sussman and Joel H. Saltz },
title = { Visualization of Large Datasets with the {Active Data Repository} },
}
@techreport { Beynon01-TR,
year = { 2001 },
number = { CS-TR-4249 and UMIACS-TR-2001-34 },
month = { May },
institution = { University of Maryland, Department of Computer Science and UMIACS },
author = { Michael D. Beynon and Tahsin M. Kurc and {\"U}mit V. \c{C}ataly\"{u}rek and Alan Sussman and Joel H. Saltz },
title = { A Component-based Implementation of Iso-surface Rendering for Visualizing Large Datasets },
annote = { DataCutter },
}
@inproceedings { Catalyurek01-Irr,
pdf = { Catalyurek01-Irr.pdf },
doi = { 10.1109/IPDPS.2001.925093 },
year = { 2001 },
month = { Apr },
key = { CATALYUREK01B },
booktitle = { Proceedings of 15th International Parallel and Distributed Processing Symposium ({IPDPS}) },
author = { {\"U}mit V. \c{C}ataly\"{u}rek and Cevdet Aykanat },
address = { San Francisco, {CA} },
title = { A Fine-Grain Hypergraph Model for {2D} Decomposition of Sparse Matrices },
}
@inproceedings { CHANG01B,
year = { 2001 },
organization = { SIAM },
month = { Mar },
booktitle = { Proceedings of the Eleventh SIAM Conference on Parallel Processing for Scientific Computing },
author = { Chialin Chang and Tahsin M. Kurc and Alan Sussman and {\"U}mit V. \c{C}ataly\"{u}rek and Joel H. Saltz },
title = { A Hypergraph-Based Workload Partitioning Strategy for Parallel Data Aggregation },
}
@techreport { Kurc01,
year = { 2001 },
number = { CS-TR-4208 and UMIACS-TR-2001-04 },
note = { Also appears in IEEE Computer Graphics and Applications, Jul/Aug 2001 },
month = { Jan },
institution = { University of Maryland, Department of Computer Science and UMIACS },
author = { Tahsin M. Kurc and {\"U}mit V. \c{C}ataly\"{u}rek and Chialin Chang and Alan Sussman and Joel H. Saltz },
title = { Exploration and Visualization of Very Large Datasets with the {Active Data Repository} },
}
@phdthesis { Catalyurek99PhD,
pdf = { Catalyurek99PhD.pdf },
year = { 1999 },
month = { Nov },
key = { Catalyurek99PhD },
institution = { Bilkent University, Computer Engineering and Information Science },
author = { {\"U}mit V. \c{C}ataly\"{u}rek },
title = { Hypergraph Models for Sparse Matrix Partitioning and Reordering },
}
@article { Catalyurek99,
pdf = { Catalyurek99.pdf },
doi = { 10.1109/71.780863 },
year = { 1999 },
volume = { 10 },
pages = { 673--693 },
number = { 7 },
key = { CATALYUREK99 },
journal = { IEEE Transactions on Parallel and Distributed Systems },
author = { {\"U}mit V. \c{C}ataly\"{u}rek and Cevdet Aykanat },
title = { Hypergraph-Partitioning Based Decomposition for Parallel Sparse-Matrix Vector Multiplication },
}
@techreport { patohmanual,
pdf = { http://cc.gatech.edu/\%7Eumit/PaToH/manual.pdf },
year = { 1999 },
url = { http://cc.gatech.edu/\%7Eumit/software.html },
address = { Ankara, 06533 Turkey },
institution = { Bilkent University, Department of Computer Engineering },
author = { {\"U}mit V. \c{C}ataly\"{u}rek and Cevdet Aykanat },
title = { {PaToH}: A Multilevel Hypergraph Partitioning Tool, Version 3.0 },
}
@article { Pinar96,
pdf = { Pinar96.pdf },
doi = { 10.1007/3-540-60902-4_50 },
year = { 1996 },
volume = { 1041 },
pages = { 473--482 },
journal = { Lecture notes in Computer Science },
author = { Ali P{\i}nar and {\"U}mit V. \c{C}ataly\"{u}rek and Cevdet Aykanat and M. P{\i}nar },
title = { Decomposing linear programs for parallel solution },
}
@inproceedings { Catalyurek96,
pdf = { Catalyurek96.pdf },
year = { 1996 },
volume = { 1117 },
series = { Lecture notes in Computer Science },
publisher = { Springer-Verlag },
pages = { 75--86 },
key = { CATALYUREK96 },
booktitle = { Proceedings of 3rd International Symposium on Solving Irregularly Structured Problems in Parallel, Irregular\'96 },
author = { {\"U}mit V. \c{C}ataly\"{u}rek and Cevdet Aykanat },
title = { Decomposing irregularly sparse matrices for parallel matrix-vector multiplications },
}
@inproceedings { Catalyurek95,
pdf = { Catalyurek95.pdf },
year = { 1995 },
month = { Dec },
booktitle = { Proceedings of International Conference on High Performance Computing },
author = { {\"U}mit V. \c{C}ataly\"{u}rek and Cevdet Aykanat },
title = { A Hypergraph Model for Mapping Repeated Sparse Matrix-Vector Product Computations onto Multicomputers },
}
@mastersthesis { Catalyurek94,
year = { 1994 },
title = { A Constructive Multi-way Circuit Partitioning Algorithm Based on Minimum Degree Ordering },
month = { Sep },
institution = { Bilkent University, Computer Engineering and Information Science },
author = { {\"U}mit V. \c{C}ataly\"{u}rek },
}